Starting phenix.real_space_refine on Sun Apr 5 22:13:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dni_30784/04_2026/7dni_30784.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dni_30784/04_2026/7dni_30784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dni_30784/04_2026/7dni_30784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dni_30784/04_2026/7dni_30784.map" model { file = "/net/cci-nas-00/data/ceres_data/7dni_30784/04_2026/7dni_30784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dni_30784/04_2026/7dni_30784.cif" } resolution = 3.2 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= 0.005 sd= 0.074 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 56 5.16 5 C 8930 2.51 5 N 2427 2.21 5 O 2664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14077 Number of models: 1 Model: "" Number of chains: 16 Chain: "H" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "F" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "J" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "K" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "A" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1594 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 191} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1582 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 190} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 1567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1567 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 189} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1570 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 189} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "E" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 574 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "G" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 593 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "I" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 574 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "L" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "M" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 91} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 91} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 773 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 91} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 91} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N LEU H 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU H 73 " occ=0.45 residue: pdb=" N LEU F 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU F 73 " occ=0.45 residue: pdb=" N LEU J 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU J 73 " occ=0.45 residue: pdb=" N LEU G 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU G 73 " occ=0.45 residue: pdb=" N LEU L 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU L 73 " occ=0.45 Time building chain proxies: 3.29, per 1000 atoms: 0.23 Number of scatterers: 14077 At special positions: 0 Unit cell: (105.545, 117.04, 113.905, 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 56 16.00 O 2664 8.00 N 2427 7.00 C 8930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 558.8 milliseconds 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3362 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 8 sheets defined 66.6% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'H' and resid 22 through 34 removed outlier: 3.553A pdb=" N ASP H 32 " --> pdb=" O ALA H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 60 Processing helix chain 'F' and resid 22 through 34 removed outlier: 3.577A pdb=" N GLN F 31 " --> pdb=" O LYS F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 39 No H-bonds generated for 'chain 'F' and resid 37 through 39' Processing helix chain 'F' and resid 55 through 60 Processing helix chain 'J' and resid 22 through 35 Processing helix chain 'J' and resid 37 through 41 Processing helix chain 'J' and resid 55 through 60 removed outlier: 3.856A pdb=" N TYR J 59 " --> pdb=" O THR J 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 35 removed outlier: 3.631A pdb=" N GLN K 31 " --> pdb=" O LYS K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 60 Processing helix chain 'A' and resid 7 through 18 removed outlier: 3.846A pdb=" N PHE A 11 " --> pdb=" O THR A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 26 removed outlier: 4.609A pdb=" N MET A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 32 Processing helix chain 'A' and resid 39 through 68 removed outlier: 3.547A pdb=" N ALA A 51 " --> pdb=" O GLN A 47 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ASN A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N MET A 56 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN A 57 " --> pdb=" O SER A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 88 through 94 removed outlier: 3.858A pdb=" N ALA A 92 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 129 Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 130 through 142 removed outlier: 5.128A pdb=" N ASP A 136 " --> pdb=" O ARG A 132 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.783A pdb=" N ASN A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 171 removed outlier: 3.689A pdb=" N GLY A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 176 through 187 removed outlier: 3.654A pdb=" N ASN A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 199 removed outlier: 3.643A pdb=" N VAL A 194 " --> pdb=" O ASN A 190 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 18 removed outlier: 3.829A pdb=" N PHE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 23 removed outlier: 3.529A pdb=" N LYS B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 35 removed outlier: 3.667A pdb=" N VAL B 31 " --> pdb=" O GLN B 27 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 32 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ASP B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR B 34 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 54 removed outlier: 3.954A pdb=" N GLN B 45 " --> pdb=" O GLU B 41 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 51 " --> pdb=" O GLN B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 68 removed outlier: 3.601A pdb=" N GLU B 60 " --> pdb=" O MET B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 86 removed outlier: 3.597A pdb=" N GLU B 78 " --> pdb=" O GLY B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 96 removed outlier: 3.667A pdb=" N ALA B 92 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 102 removed outlier: 4.280A pdb=" N ASP B 101 " --> pdb=" O GLU B 98 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 102 " --> pdb=" O LEU B 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 98 through 102' Processing helix chain 'B' and resid 104 through 121 Processing helix chain 'B' and resid 121 through 129 Processing helix chain 'B' and resid 134 through 142 removed outlier: 4.008A pdb=" N GLU B 140 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 Processing helix chain 'B' and resid 159 through 171 removed outlier: 3.546A pdb=" N GLY B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 176 through 188 Processing helix chain 'B' and resid 190 through 199 removed outlier: 3.905A pdb=" N VAL B 194 " --> pdb=" O ASN B 190 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN B 195 " --> pdb=" O ASN B 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 26 removed outlier: 3.802A pdb=" N ASN C 10 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ALA C 20 " --> pdb=" O SER C 16 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ARG C 21 " --> pdb=" O CYS C 17 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 32 removed outlier: 3.634A pdb=" N VAL C 31 " --> pdb=" O GLN C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 54 removed outlier: 3.879A pdb=" N GLN C 45 " --> pdb=" O GLU C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 69 removed outlier: 3.865A pdb=" N GLY C 69 " --> pdb=" O THR C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 86 removed outlier: 3.782A pdb=" N GLU C 78 " --> pdb=" O GLY C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 96 removed outlier: 3.550A pdb=" N ALA C 92 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR C 94 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 121 Processing helix chain 'C' and resid 121 through 128 Processing helix chain 'C' and resid 130 through 134 Processing helix chain 'C' and resid 135 through 141 removed outlier: 3.666A pdb=" N GLU C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 156 Processing helix chain 'C' and resid 159 through 172 removed outlier: 3.980A pdb=" N VAL C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 188 Processing helix chain 'C' and resid 190 through 198 removed outlier: 3.712A pdb=" N VAL C 194 " --> pdb=" O ASN C 190 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN C 195 " --> pdb=" O ASN C 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 26 removed outlier: 5.819A pdb=" N ALA D 20 " --> pdb=" O SER D 16 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG D 21 " --> pdb=" O CYS D 17 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 35 removed outlier: 3.778A pdb=" N VAL D 31 " --> pdb=" O GLN D 27 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASP D 33 " --> pdb=" O GLU D 29 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N TYR D 34 " --> pdb=" O PRO D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 54 removed outlier: 3.507A pdb=" N GLU D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA D 51 " --> pdb=" O GLN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 68 Processing helix chain 'D' and resid 74 through 85 removed outlier: 3.603A pdb=" N GLU D 78 " --> pdb=" O GLY D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 96 removed outlier: 3.630A pdb=" N ALA D 92 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR D 94 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN D 96 " --> pdb=" O ALA D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 129 removed outlier: 4.302A pdb=" N LEU D 115 " --> pdb=" O HIS D 111 " (cutoff:3.500A) Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 130 through 141 removed outlier: 4.784A pdb=" N ASP D 136 " --> pdb=" O ARG D 132 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LYS D 137 " --> pdb=" O ASP D 133 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU D 140 " --> pdb=" O ASP D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 156 Processing helix chain 'D' and resid 159 through 172 removed outlier: 3.573A pdb=" N LYS D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL D 172 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 188 removed outlier: 3.593A pdb=" N ASN D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 199 Processing helix chain 'E' and resid 22 through 34 Processing helix chain 'E' and resid 55 through 60 Processing helix chain 'G' and resid 22 through 34 Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 55 through 60 removed outlier: 3.788A pdb=" N TYR G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 35 Processing helix chain 'I' and resid 37 through 39 No H-bonds generated for 'chain 'I' and resid 37 through 39' Processing helix chain 'I' and resid 55 through 60 Processing helix chain 'L' and resid 22 through 32 removed outlier: 3.572A pdb=" N VAL L 26 " --> pdb=" O THR L 22 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE L 30 " --> pdb=" O VAL L 26 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN L 31 " --> pdb=" O LYS L 27 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 60 Processing helix chain 'M' and resid 3 through 15 Processing helix chain 'M' and resid 16 through 20 removed outlier: 3.577A pdb=" N CYS M 20 " --> pdb=" O SER M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 31 removed outlier: 4.533A pdb=" N LEU M 28 " --> pdb=" O VAL M 25 " (cutoff:3.500A) Proline residue: M 29 - end of helix Processing helix chain 'M' and resid 35 through 49 removed outlier: 3.600A pdb=" N ARG M 43 " --> pdb=" O GLN M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 63 removed outlier: 4.567A pdb=" N TRP M 56 " --> pdb=" O ARG M 52 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N HIS M 57 " --> pdb=" O ASP M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 79 removed outlier: 4.194A pdb=" N TYR M 71 " --> pdb=" O GLY M 67 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA M 74 " --> pdb=" O GLU M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 96 removed outlier: 3.610A pdb=" N TYR M 95 " --> pdb=" O VAL M 91 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 15 Processing helix chain 'N' and resid 16 through 22 removed outlier: 3.713A pdb=" N CYS N 20 " --> pdb=" O SER N 17 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ASN N 21 " --> pdb=" O ASN N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 31 removed outlier: 4.345A pdb=" N LEU N 28 " --> pdb=" O VAL N 25 " (cutoff:3.500A) Proline residue: N 29 - end of helix Processing helix chain 'N' and resid 35 through 49 Processing helix chain 'N' and resid 54 through 63 Processing helix chain 'N' and resid 67 through 79 removed outlier: 3.644A pdb=" N TYR N 71 " --> pdb=" O GLY N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 93 removed outlier: 4.117A pdb=" N GLU N 87 " --> pdb=" O ASP N 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 15 Processing helix chain 'O' and resid 16 through 22 removed outlier: 4.269A pdb=" N ASN O 21 " --> pdb=" O ASN O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 31 removed outlier: 4.468A pdb=" N LEU O 28 " --> pdb=" O VAL O 25 " (cutoff:3.500A) Proline residue: O 29 - end of helix Processing helix chain 'O' and resid 35 through 49 Processing helix chain 'O' and resid 51 through 63 removed outlier: 4.543A pdb=" N TRP O 56 " --> pdb=" O ARG O 52 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N HIS O 57 " --> pdb=" O ASP O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 79 removed outlier: 3.540A pdb=" N TYR O 71 " --> pdb=" O GLY O 67 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA O 74 " --> pdb=" O GLU O 70 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 93 removed outlier: 3.630A pdb=" N ALA O 85 " --> pdb=" O LEU O 81 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU O 87 " --> pdb=" O ASP O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 94 through 96 No H-bonds generated for 'chain 'O' and resid 94 through 96' Processing helix chain 'P' and resid 3 through 15 Processing helix chain 'P' and resid 16 through 22 removed outlier: 4.066A pdb=" N CYS P 20 " --> pdb=" O SER P 17 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN P 21 " --> pdb=" O ASN P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 23 through 31 removed outlier: 4.244A pdb=" N LEU P 28 " --> pdb=" O VAL P 25 " (cutoff:3.500A) Proline residue: P 29 - end of helix Processing helix chain 'P' and resid 35 through 49 removed outlier: 3.637A pdb=" N ASP P 40 " --> pdb=" O ALA P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 63 removed outlier: 4.169A pdb=" N TRP P 56 " --> pdb=" O ARG P 52 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N HIS P 57 " --> pdb=" O ASP P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 77 removed outlier: 3.634A pdb=" N TYR P 71 " --> pdb=" O GLY P 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 80 No H-bonds generated for 'chain 'P' and resid 78 through 80' Processing helix chain 'P' and resid 81 through 94 removed outlier: 4.432A pdb=" N GLU P 87 " --> pdb=" O ASP P 83 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL P 88 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER P 94 " --> pdb=" O SER P 90 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 12 through 16 removed outlier: 7.457A pdb=" N GLN H 2 " --> pdb=" O SER H 65 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N LEU H 67 " --> pdb=" O GLN H 2 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N PHE H 4 " --> pdb=" O LEU H 67 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU H 69 " --> pdb=" O PHE H 4 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LYS H 6 " --> pdb=" O LEU H 69 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N LEU H 71 " --> pdb=" O LYS H 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 12 through 16 removed outlier: 3.660A pdb=" N ILE F 13 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N LEU F 67 " --> pdb=" O GLN F 2 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N PHE F 4 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU F 69 " --> pdb=" O PHE F 4 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LYS F 6 " --> pdb=" O LEU F 69 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N LEU F 71 " --> pdb=" O LYS F 6 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL F 70 " --> pdb=" O ARG F 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 12 through 16 removed outlier: 7.255A pdb=" N GLN J 2 " --> pdb=" O SER J 65 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N LEU J 67 " --> pdb=" O GLN J 2 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N PHE J 4 " --> pdb=" O LEU J 67 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU J 69 " --> pdb=" O PHE J 4 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LYS J 6 " --> pdb=" O LEU J 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 13 through 16 removed outlier: 3.744A pdb=" N SER K 65 " --> pdb=" O GLN K 2 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 12 through 16 Processing sheet with id=AA6, first strand: chain 'G' and resid 12 through 15 removed outlier: 3.729A pdb=" N VAL G 70 " --> pdb=" O ARG G 42 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 14 through 16 removed outlier: 3.624A pdb=" N VAL I 70 " --> pdb=" O ARG I 42 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 12 through 16 removed outlier: 3.535A pdb=" N VAL L 70 " --> pdb=" O ARG L 42 " (cutoff:3.500A) 728 hydrogen bonds defined for protein. 2061 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.07 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2428 1.32 - 1.44: 3518 1.44 - 1.56: 8282 1.56 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 14312 Sorted by residual: bond pdb=" C PRO L 37 " pdb=" O PRO L 37 " ideal model delta sigma weight residual 1.243 1.200 0.044 8.50e-03 1.38e+04 2.63e+01 bond pdb=" C PRO E 19 " pdb=" O PRO E 19 " ideal model delta sigma weight residual 1.237 1.196 0.042 1.28e-02 6.10e+03 1.06e+01 bond pdb=" C PRO L 38 " pdb=" O PRO L 38 " ideal model delta sigma weight residual 1.238 1.197 0.041 1.33e-02 5.65e+03 9.48e+00 bond pdb=" N GLU D 166 " pdb=" CA GLU D 166 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.27e-02 6.20e+03 6.21e+00 bond pdb=" CA ALA H 46 " pdb=" CB ALA H 46 " ideal model delta sigma weight residual 1.527 1.485 0.042 1.70e-02 3.46e+03 6.08e+00 ... (remaining 14307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 18699 2.05 - 4.11: 606 4.11 - 6.16: 78 6.16 - 8.21: 9 8.21 - 10.27: 3 Bond angle restraints: 19395 Sorted by residual: angle pdb=" N PRO L 37 " pdb=" CA PRO L 37 " pdb=" CB PRO L 37 " ideal model delta sigma weight residual 103.22 106.69 -3.47 5.20e-01 3.70e+00 4.47e+01 angle pdb=" C LYS F 48 " pdb=" CA LYS F 48 " pdb=" CB LYS F 48 " ideal model delta sigma weight residual 110.34 102.57 7.77 1.40e+00 5.10e-01 3.08e+01 angle pdb=" C THR D 124 " pdb=" CA THR D 124 " pdb=" CB THR D 124 " ideal model delta sigma weight residual 110.90 102.79 8.11 1.58e+00 4.01e-01 2.64e+01 angle pdb=" N PRO E 19 " pdb=" CA PRO E 19 " pdb=" C PRO E 19 " ideal model delta sigma weight residual 113.86 107.77 6.09 1.25e+00 6.40e-01 2.37e+01 angle pdb=" N GLY F 35 " pdb=" CA GLY F 35 " pdb=" C GLY F 35 " ideal model delta sigma weight residual 113.18 123.45 -10.27 2.37e+00 1.78e-01 1.88e+01 ... (remaining 19390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 7886 17.66 - 35.32: 699 35.32 - 52.98: 131 52.98 - 70.64: 21 70.64 - 88.30: 18 Dihedral angle restraints: 8755 sinusoidal: 3592 harmonic: 5163 Sorted by residual: dihedral pdb=" CA GLN E 41 " pdb=" C GLN E 41 " pdb=" N ARG E 42 " pdb=" CA ARG E 42 " ideal model delta harmonic sigma weight residual 180.00 158.23 21.77 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA GLU J 34 " pdb=" C GLU J 34 " pdb=" N GLY J 35 " pdb=" CA GLY J 35 " ideal model delta harmonic sigma weight residual 180.00 158.42 21.58 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" C LYS F 48 " pdb=" N LYS F 48 " pdb=" CA LYS F 48 " pdb=" CB LYS F 48 " ideal model delta harmonic sigma weight residual -122.60 -112.24 -10.36 0 2.50e+00 1.60e-01 1.72e+01 ... (remaining 8752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1717 0.057 - 0.114: 468 0.114 - 0.171: 62 0.171 - 0.228: 6 0.228 - 0.285: 2 Chirality restraints: 2255 Sorted by residual: chirality pdb=" CA LYS F 48 " pdb=" N LYS F 48 " pdb=" C LYS F 48 " pdb=" CB LYS F 48 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA GLU E 51 " pdb=" N GLU E 51 " pdb=" C GLU E 51 " pdb=" CB GLU E 51 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA LYS H 48 " pdb=" N LYS H 48 " pdb=" C LYS H 48 " pdb=" CB LYS H 48 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2252 not shown) Planarity restraints: 2497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP P 86 " 0.021 2.00e-02 2.50e+03 4.33e-02 1.87e+01 pdb=" C ASP P 86 " -0.075 2.00e-02 2.50e+03 pdb=" O ASP P 86 " 0.028 2.00e-02 2.50e+03 pdb=" N GLU P 87 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO K 37 " 0.060 5.00e-02 4.00e+02 8.95e-02 1.28e+01 pdb=" N PRO K 38 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO K 38 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO K 38 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU L 18 " 0.051 5.00e-02 4.00e+02 7.75e-02 9.62e+00 pdb=" N PRO L 19 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO L 19 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO L 19 " 0.043 5.00e-02 4.00e+02 ... (remaining 2494 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1898 2.74 - 3.28: 15246 3.28 - 3.82: 23496 3.82 - 4.36: 29405 4.36 - 4.90: 49030 Nonbonded interactions: 119075 Sorted by model distance: nonbonded pdb=" NE2 GLN G 2 " pdb=" OG1 THR G 14 " model vdw 2.196 3.120 nonbonded pdb=" NH1 ARG B 12 " pdb=" O GLU B 67 " model vdw 2.202 3.120 nonbonded pdb=" OG1 THR E 22 " pdb=" O GLY E 53 " model vdw 2.203 3.040 nonbonded pdb=" N MET E 1 " pdb=" O VAL E 17 " model vdw 2.213 3.120 nonbonded pdb=" OG1 THR L 22 " pdb=" OE1 GLU L 24 " model vdw 2.213 3.040 ... (remaining 119070 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 4 through 100 or (resid 101 and (name N or name CA or name \ C or name O or name CB )) or resid 102 through 131 or (resid 132 and (name N or \ name CA or name C or name O or name CB )) or resid 133 through 186 or (resid 18 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 188 through \ 200)) selection = (chain 'B' and (resid 4 through 100 or (resid 101 and (name N or name CA or name \ C or name O or name CB )) or resid 102 through 186 or (resid 187 and (name N or \ name CA or name C or name O or name CB )) or resid 188 through 200)) selection = chain 'C' selection = (chain 'D' and (resid 4 through 100 or (resid 101 and (name N or name CA or name \ C or name O or name CB )) or resid 102 through 200)) } ncs_group { reference = chain 'E' selection = (chain 'F' and resid 1 through 72) selection = (chain 'G' and resid 1 through 72) selection = (chain 'H' and resid 1 through 72) selection = chain 'I' selection = (chain 'J' and resid 1 through 72) selection = (chain 'K' and resid 1 through 72) selection = (chain 'L' and resid 1 through 72) } ncs_group { reference = (chain 'M' and resid 1 through 96) selection = (chain 'N' and resid 1 through 96) selection = chain 'O' selection = (chain 'P' and resid 1 through 96) } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.940 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 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 : 0.009 0.079 14312 Z= 0.400 Angle : 0.842 10.266 19395 Z= 0.482 Chirality : 0.052 0.285 2255 Planarity : 0.005 0.090 2497 Dihedral : 14.309 88.302 5393 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.90 % Allowed : 0.71 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.20), residues: 1729 helix: -1.57 (0.15), residues: 999 sheet: -1.66 (0.36), residues: 198 loop : 0.67 (0.29), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 42 TYR 0.034 0.002 TYR O 95 PHE 0.016 0.002 PHE C 107 TRP 0.011 0.002 TRP D 177 HIS 0.008 0.002 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00900 (14312) covalent geometry : angle 0.84203 (19395) hydrogen bonds : bond 0.25785 ( 728) hydrogen bonds : angle 9.79191 ( 2061) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 405 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 1 MET cc_start: 0.7600 (ttp) cc_final: 0.7180 (ttm) REVERT: H 18 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8072 (tm-30) REVERT: H 20 SER cc_start: 0.9156 (p) cc_final: 0.8795 (p) REVERT: H 31 GLN cc_start: 0.8631 (tp40) cc_final: 0.8357 (tp40) REVERT: F 41 GLN cc_start: 0.7577 (mt0) cc_final: 0.7157 (mt0) REVERT: F 63 LYS cc_start: 0.9276 (ptpt) cc_final: 0.9058 (pttp) REVERT: F 65 SER cc_start: 0.8503 (m) cc_final: 0.8206 (m) REVERT: J 1 MET cc_start: 0.8497 (ttp) cc_final: 0.8246 (ttp) REVERT: J 30 ILE cc_start: 0.9625 (mp) cc_final: 0.9425 (mp) REVERT: J 31 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8503 (tm-30) REVERT: K 2 GLN cc_start: 0.8176 (pt0) cc_final: 0.7924 (pt0) REVERT: K 4 PHE cc_start: 0.7893 (m-10) cc_final: 0.7461 (m-10) REVERT: K 34 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7897 (mp0) REVERT: A 24 MET cc_start: 0.8960 (mtm) cc_final: 0.8736 (mtp) REVERT: A 136 ASP cc_start: 0.7832 (t0) cc_final: 0.7208 (t0) REVERT: B 8 ASP cc_start: 0.8162 (t70) cc_final: 0.7805 (t0) REVERT: B 60 GLU cc_start: 0.8382 (tp30) cc_final: 0.8151 (tm-30) REVERT: B 101 ASP cc_start: 0.8299 (t0) cc_final: 0.7913 (t0) REVERT: B 127 ASP cc_start: 0.8324 (m-30) cc_final: 0.7945 (m-30) REVERT: C 166 GLU cc_start: 0.8782 (tp30) cc_final: 0.8385 (tp30) REVERT: D 41 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8343 (tm-30) REVERT: D 112 ASP cc_start: 0.8548 (t0) cc_final: 0.8287 (t0) REVERT: D 137 LYS cc_start: 0.9015 (tppp) cc_final: 0.8751 (tppt) REVERT: E 48 LYS cc_start: 0.8590 (tttp) cc_final: 0.8115 (tptt) REVERT: G 24 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8466 (mm-30) REVERT: G 31 GLN cc_start: 0.9509 (tt0) cc_final: 0.9302 (tt0) REVERT: G 32 ASP cc_start: 0.8476 (m-30) cc_final: 0.8135 (m-30) REVERT: G 34 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7695 (mm-30) REVERT: G 52 ASP cc_start: 0.8715 (m-30) cc_final: 0.8358 (m-30) REVERT: I 2 GLN cc_start: 0.7511 (tp-100) cc_final: 0.7210 (tp40) REVERT: L 18 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8576 (tm-30) REVERT: L 31 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7780 (mp10) REVERT: L 51 GLU cc_start: 0.6369 (mp0) cc_final: 0.5845 (mp0) REVERT: M 6 ASP cc_start: 0.8750 (t70) cc_final: 0.8512 (t0) REVERT: M 82 VAL cc_start: 0.9051 (t) cc_final: 0.8670 (t) REVERT: N 86 ASP cc_start: 0.8584 (p0) cc_final: 0.8338 (p0) REVERT: N 90 SER cc_start: 0.9018 (m) cc_final: 0.8816 (m) REVERT: N 93 GLN cc_start: 0.8732 (pm20) cc_final: 0.8473 (pm20) REVERT: O 15 ASN cc_start: 0.8908 (m-40) cc_final: 0.8600 (m-40) REVERT: O 93 GLN cc_start: 0.9158 (pp30) cc_final: 0.8948 (pp30) REVERT: O 95 TYR cc_start: 0.7587 (t80) cc_final: 0.6800 (t80) REVERT: P 6 ASP cc_start: 0.8370 (t0) cc_final: 0.8133 (t0) REVERT: P 38 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7524 (m-30) REVERT: P 65 ARG cc_start: 0.8387 (mmt-90) cc_final: 0.8074 (mpt180) REVERT: P 95 TYR cc_start: 0.7145 (t80) cc_final: 0.6790 (t80) outliers start: 14 outliers final: 2 residues processed: 408 average time/residue: 0.1437 time to fit residues: 81.6256 Evaluate side-chains 344 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 339 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 31 GLN Chi-restraints excluded: chain P residue 38 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.0670 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 40 GLN F 41 GLN B 195 GLN D 10 ASN E 40 GLN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN ** O 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 15 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.090528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.070897 restraints weight = 30511.136| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.59 r_work: 0.2902 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14312 Z= 0.151 Angle : 0.669 9.661 19395 Z= 0.351 Chirality : 0.044 0.209 2255 Planarity : 0.005 0.058 2497 Dihedral : 5.504 56.043 1922 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.22 % Allowed : 11.25 % Favored : 87.52 % 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: -0.83 (0.20), residues: 1729 helix: -0.60 (0.15), residues: 1046 sheet: -1.77 (0.35), residues: 198 loop : 0.72 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 52 TYR 0.015 0.001 TYR B 13 PHE 0.018 0.001 PHE A 107 TRP 0.010 0.001 TRP O 56 HIS 0.005 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00335 (14312) covalent geometry : angle 0.66928 (19395) hydrogen bonds : bond 0.04934 ( 728) hydrogen bonds : angle 5.73965 ( 2061) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 398 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8112 (tm-30) REVERT: H 21 ASP cc_start: 0.8410 (m-30) cc_final: 0.7902 (m-30) REVERT: H 60 ASN cc_start: 0.9024 (t0) cc_final: 0.8781 (p0) REVERT: F 25 ASN cc_start: 0.8493 (t0) cc_final: 0.8192 (t0) REVERT: J 18 GLU cc_start: 0.8708 (mp0) cc_final: 0.8209 (mp0) REVERT: J 31 GLN cc_start: 0.8861 (tm-30) cc_final: 0.8569 (tm-30) REVERT: K 62 GLN cc_start: 0.7595 (pp30) cc_final: 0.7303 (pp30) REVERT: A 112 ASP cc_start: 0.8403 (m-30) cc_final: 0.8172 (m-30) REVERT: B 8 ASP cc_start: 0.8294 (t70) cc_final: 0.7915 (t0) REVERT: B 68 LYS cc_start: 0.8945 (ptpp) cc_final: 0.8650 (ptpp) REVERT: B 101 ASP cc_start: 0.7897 (t0) cc_final: 0.7483 (t0) REVERT: B 127 ASP cc_start: 0.8189 (m-30) cc_final: 0.7954 (m-30) REVERT: B 170 ARG cc_start: 0.8566 (mmt90) cc_final: 0.8133 (mmm-85) REVERT: D 41 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8109 (tm-30) REVERT: D 112 ASP cc_start: 0.8562 (t0) cc_final: 0.8310 (t0) REVERT: E 4 PHE cc_start: 0.7845 (m-80) cc_final: 0.7550 (m-10) REVERT: E 48 LYS cc_start: 0.9111 (tttp) cc_final: 0.8704 (tptt) REVERT: G 24 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8417 (mm-30) REVERT: G 34 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7329 (mm-30) REVERT: G 42 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.7621 (mtm180) REVERT: L 24 GLU cc_start: 0.8096 (mp0) cc_final: 0.7774 (mp0) REVERT: L 64 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8068 (tm-30) REVERT: N 86 ASP cc_start: 0.8437 (p0) cc_final: 0.8225 (p0) REVERT: O 93 GLN cc_start: 0.8986 (pp30) cc_final: 0.8747 (pp30) REVERT: P 6 ASP cc_start: 0.8432 (t0) cc_final: 0.8075 (t0) outliers start: 19 outliers final: 9 residues processed: 408 average time/residue: 0.1284 time to fit residues: 74.9141 Evaluate side-chains 350 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 339 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain J residue 54 ARG Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 88 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 8 optimal weight: 20.0000 chunk 110 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 129 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 49 GLN K 2 GLN K 60 ASN A 150 ASN G 49 GLN L 68 HIS ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.088390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.068464 restraints weight = 31352.341| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.73 r_work: 0.2857 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 14312 Z= 0.220 Angle : 0.659 7.952 19395 Z= 0.338 Chirality : 0.045 0.199 2255 Planarity : 0.005 0.056 2497 Dihedral : 5.001 48.764 1914 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.83 % Allowed : 14.47 % Favored : 82.70 % 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: -0.54 (0.20), residues: 1729 helix: -0.30 (0.16), residues: 1038 sheet: -1.65 (0.35), residues: 193 loop : 0.62 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 41 TYR 0.029 0.002 TYR P 95 PHE 0.022 0.002 PHE P 3 TRP 0.007 0.001 TRP O 56 HIS 0.007 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00527 (14312) covalent geometry : angle 0.65902 (19395) hydrogen bonds : bond 0.04259 ( 728) hydrogen bonds : angle 5.33972 ( 2061) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 361 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.7840 (tm-30) REVERT: H 21 ASP cc_start: 0.8444 (m-30) cc_final: 0.7727 (m-30) REVERT: H 31 GLN cc_start: 0.8822 (tp40) cc_final: 0.8276 (tp40) REVERT: H 60 ASN cc_start: 0.9058 (t0) cc_final: 0.8539 (p0) REVERT: F 25 ASN cc_start: 0.8520 (t0) cc_final: 0.8275 (t0) REVERT: F 34 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8204 (tm-30) REVERT: J 18 GLU cc_start: 0.8852 (mp0) cc_final: 0.8432 (mp0) REVERT: J 31 GLN cc_start: 0.8958 (tm-30) cc_final: 0.8633 (tm-30) REVERT: K 11 LYS cc_start: 0.8362 (tmtt) cc_final: 0.8093 (tmtt) REVERT: A 25 TYR cc_start: 0.9303 (m-10) cc_final: 0.9001 (m-10) REVERT: A 47 GLN cc_start: 0.8560 (tp-100) cc_final: 0.8340 (mm-40) REVERT: B 8 ASP cc_start: 0.8304 (t70) cc_final: 0.7983 (t0) REVERT: B 95 MET cc_start: 0.9052 (mmt) cc_final: 0.8842 (mmt) REVERT: B 101 ASP cc_start: 0.8177 (t0) cc_final: 0.7818 (t0) REVERT: B 118 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8731 (tt) REVERT: B 127 ASP cc_start: 0.8428 (m-30) cc_final: 0.8158 (m-30) REVERT: B 170 ARG cc_start: 0.8626 (mmt90) cc_final: 0.8322 (mmm-85) REVERT: C 112 ASP cc_start: 0.9015 (m-30) cc_final: 0.8761 (m-30) REVERT: D 41 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8205 (tm-30) REVERT: D 112 ASP cc_start: 0.8766 (t0) cc_final: 0.8470 (t0) REVERT: D 137 LYS cc_start: 0.9266 (tppp) cc_final: 0.8959 (tppt) REVERT: E 4 PHE cc_start: 0.7924 (m-80) cc_final: 0.7712 (m-80) REVERT: E 11 LYS cc_start: 0.8178 (pptt) cc_final: 0.7946 (ptpp) REVERT: E 21 ASP cc_start: 0.7385 (p0) cc_final: 0.7164 (p0) REVERT: E 48 LYS cc_start: 0.9076 (tttp) cc_final: 0.8676 (tptt) REVERT: G 2 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7736 (tm-30) REVERT: G 42 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7520 (mtm180) REVERT: G 63 LYS cc_start: 0.9015 (mtpt) cc_final: 0.8680 (mtpt) REVERT: G 72 ARG cc_start: 0.8147 (ttm-80) cc_final: 0.7753 (ttm-80) REVERT: I 41 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7321 (pm20) REVERT: L 64 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8135 (tm-30) REVERT: M 14 ARG cc_start: 0.8397 (mtm110) cc_final: 0.8151 (ttp-110) REVERT: N 11 TYR cc_start: 0.8958 (t80) cc_final: 0.8730 (t80) REVERT: O 93 GLN cc_start: 0.9124 (pp30) cc_final: 0.8871 (pp30) REVERT: O 95 TYR cc_start: 0.7987 (t80) cc_final: 0.6731 (t80) REVERT: P 6 ASP cc_start: 0.8413 (t0) cc_final: 0.8171 (t0) outliers start: 44 outliers final: 22 residues processed: 391 average time/residue: 0.1277 time to fit residues: 71.3046 Evaluate side-chains 360 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 334 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 17 SER Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 88 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 55 optimal weight: 0.9980 chunk 134 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 126 optimal weight: 0.0470 chunk 114 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 156 optimal weight: 0.0570 chunk 6 optimal weight: 0.9980 chunk 129 optimal weight: 0.1980 chunk 112 optimal weight: 20.0000 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 GLN K 25 ASN A 47 GLN A 116 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.091723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.071864 restraints weight = 30696.731| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.76 r_work: 0.2929 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14312 Z= 0.119 Angle : 0.594 8.339 19395 Z= 0.312 Chirality : 0.042 0.197 2255 Planarity : 0.004 0.057 2497 Dihedral : 4.797 50.973 1914 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.93 % Allowed : 17.49 % Favored : 80.58 % 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 (0.21), residues: 1729 helix: 0.12 (0.16), residues: 1031 sheet: -1.62 (0.35), residues: 198 loop : 0.67 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 54 TYR 0.033 0.001 TYR P 95 PHE 0.018 0.001 PHE P 3 TRP 0.009 0.001 TRP M 56 HIS 0.006 0.001 HIS C 111 Details of bonding type rmsd covalent geometry : bond 0.00264 (14312) covalent geometry : angle 0.59357 (19395) hydrogen bonds : bond 0.03399 ( 728) hydrogen bonds : angle 4.87818 ( 2061) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 390 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 16 GLU cc_start: 0.7987 (tp30) cc_final: 0.7566 (tp30) REVERT: H 21 ASP cc_start: 0.8422 (m-30) cc_final: 0.7983 (m-30) REVERT: H 41 GLN cc_start: 0.8904 (mp10) cc_final: 0.8181 (mp10) REVERT: H 60 ASN cc_start: 0.8998 (t0) cc_final: 0.8503 (p0) REVERT: K 11 LYS cc_start: 0.8301 (tmtt) cc_final: 0.8089 (tmtt) REVERT: K 62 GLN cc_start: 0.7722 (pp30) cc_final: 0.7466 (pp30) REVERT: A 25 TYR cc_start: 0.9288 (m-10) cc_final: 0.8983 (m-10) REVERT: A 47 GLN cc_start: 0.8353 (tp40) cc_final: 0.8148 (mm-40) REVERT: A 136 ASP cc_start: 0.7292 (t0) cc_final: 0.6463 (t0) REVERT: B 8 ASP cc_start: 0.8300 (t70) cc_final: 0.7951 (t0) REVERT: B 95 MET cc_start: 0.8923 (mmt) cc_final: 0.8423 (mmp) REVERT: B 101 ASP cc_start: 0.8099 (t0) cc_final: 0.7721 (t0) REVERT: B 127 ASP cc_start: 0.8345 (m-30) cc_final: 0.8093 (m-30) REVERT: B 147 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8418 (tp30) REVERT: C 112 ASP cc_start: 0.9044 (m-30) cc_final: 0.8703 (m-30) REVERT: C 158 ASN cc_start: 0.8789 (p0) cc_final: 0.8547 (p0) REVERT: D 13 TYR cc_start: 0.8710 (t80) cc_final: 0.8295 (t80) REVERT: D 41 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8098 (tm-30) REVERT: D 56 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8111 (mtt) REVERT: D 112 ASP cc_start: 0.8650 (t0) cc_final: 0.8352 (t0) REVERT: E 4 PHE cc_start: 0.7816 (m-80) cc_final: 0.7605 (m-80) REVERT: E 11 LYS cc_start: 0.8124 (pptt) cc_final: 0.7912 (ptpp) REVERT: E 48 LYS cc_start: 0.9127 (tttp) cc_final: 0.8738 (tptt) REVERT: G 1 MET cc_start: 0.7666 (ttp) cc_final: 0.7442 (ttp) REVERT: G 6 LYS cc_start: 0.8887 (mtpp) cc_final: 0.8616 (mtpp) REVERT: G 42 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7549 (mtm180) REVERT: G 63 LYS cc_start: 0.8960 (mtpt) cc_final: 0.8450 (mtpt) REVERT: I 1 MET cc_start: 0.7703 (tpt) cc_final: 0.7404 (tpt) REVERT: I 41 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7366 (pm20) REVERT: L 16 GLU cc_start: 0.8658 (mp0) cc_final: 0.8355 (mp0) REVERT: L 24 GLU cc_start: 0.8244 (mp0) cc_final: 0.7914 (mp0) REVERT: L 60 ASN cc_start: 0.8369 (t0) cc_final: 0.8075 (t0) REVERT: L 62 GLN cc_start: 0.8490 (mp10) cc_final: 0.8188 (mp10) REVERT: L 64 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8093 (tm-30) REVERT: M 14 ARG cc_start: 0.8335 (mtm110) cc_final: 0.7949 (ttp80) REVERT: M 87 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8390 (tm-30) REVERT: N 1 MET cc_start: 0.6427 (tpp) cc_final: 0.5758 (tpp) REVERT: N 11 TYR cc_start: 0.8876 (t80) cc_final: 0.8665 (t80) REVERT: N 14 ARG cc_start: 0.8540 (tpp80) cc_final: 0.8194 (tpp80) REVERT: O 1 MET cc_start: 0.7547 (tpp) cc_final: 0.7269 (mmm) REVERT: O 40 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8232 (m-30) REVERT: O 86 ASP cc_start: 0.9245 (OUTLIER) cc_final: 0.8957 (t0) REVERT: O 93 GLN cc_start: 0.9168 (pp30) cc_final: 0.8875 (pp30) REVERT: O 95 TYR cc_start: 0.7896 (t80) cc_final: 0.6998 (t80) REVERT: P 6 ASP cc_start: 0.8368 (t0) cc_final: 0.8154 (t0) REVERT: P 49 SER cc_start: 0.9352 (m) cc_final: 0.8802 (p) outliers start: 30 outliers final: 12 residues processed: 413 average time/residue: 0.1330 time to fit residues: 78.2887 Evaluate side-chains 360 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 342 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain O residue 40 ASP Chi-restraints excluded: chain O residue 86 ASP Chi-restraints excluded: chain P residue 55 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 127 optimal weight: 8.9990 chunk 102 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 143 optimal weight: 0.0770 chunk 105 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 49 GLN K 2 GLN D 111 HIS ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 HIS L 25 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.091781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.072042 restraints weight = 30681.679| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.75 r_work: 0.2923 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14312 Z= 0.122 Angle : 0.592 8.089 19395 Z= 0.308 Chirality : 0.042 0.177 2255 Planarity : 0.004 0.048 2497 Dihedral : 4.705 52.468 1914 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.93 % Allowed : 21.29 % Favored : 76.78 % 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: 0.01 (0.21), residues: 1729 helix: 0.24 (0.16), residues: 1040 sheet: -1.40 (0.35), residues: 196 loop : 0.59 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 54 TYR 0.036 0.001 TYR P 95 PHE 0.015 0.001 PHE A 107 TRP 0.008 0.001 TRP O 56 HIS 0.007 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00279 (14312) covalent geometry : angle 0.59204 (19395) hydrogen bonds : bond 0.03281 ( 728) hydrogen bonds : angle 4.74563 ( 2061) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 374 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 16 GLU cc_start: 0.7980 (tp30) cc_final: 0.7544 (tp30) REVERT: H 18 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.7968 (tm-30) REVERT: H 21 ASP cc_start: 0.8412 (m-30) cc_final: 0.7914 (m-30) REVERT: H 31 GLN cc_start: 0.8697 (tp40) cc_final: 0.8194 (tp40) REVERT: H 41 GLN cc_start: 0.8885 (mp10) cc_final: 0.8096 (mp10) REVERT: H 60 ASN cc_start: 0.8977 (t0) cc_final: 0.8514 (p0) REVERT: J 18 GLU cc_start: 0.8866 (mp0) cc_final: 0.8486 (mp0) REVERT: J 21 ASP cc_start: 0.8126 (m-30) cc_final: 0.7110 (m-30) REVERT: K 51 GLU cc_start: 0.8379 (tp30) cc_final: 0.7924 (mm-30) REVERT: K 62 GLN cc_start: 0.7790 (pp30) cc_final: 0.7501 (pp30) REVERT: A 25 TYR cc_start: 0.9280 (m-10) cc_final: 0.8964 (m-10) REVERT: A 138 CYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8561 (m) REVERT: A 187 GLN cc_start: 0.8736 (mt0) cc_final: 0.8423 (mt0) REVERT: B 8 ASP cc_start: 0.8300 (t70) cc_final: 0.7971 (t0) REVERT: B 95 MET cc_start: 0.8917 (mmt) cc_final: 0.8486 (mmp) REVERT: B 101 ASP cc_start: 0.8082 (t0) cc_final: 0.7776 (t0) REVERT: B 127 ASP cc_start: 0.8332 (m-30) cc_final: 0.8067 (m-30) REVERT: B 147 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8460 (tp30) REVERT: C 112 ASP cc_start: 0.9070 (m-30) cc_final: 0.8721 (m-30) REVERT: C 158 ASN cc_start: 0.8746 (p0) cc_final: 0.8500 (p0) REVERT: D 13 TYR cc_start: 0.8796 (t80) cc_final: 0.8479 (t80) REVERT: D 41 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8102 (tm-30) REVERT: D 56 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.8128 (mtt) REVERT: D 60 GLU cc_start: 0.8291 (tt0) cc_final: 0.8045 (tt0) REVERT: E 51 GLU cc_start: 0.8480 (tp30) cc_final: 0.7897 (tp30) REVERT: E 52 ASP cc_start: 0.8188 (p0) cc_final: 0.7956 (p0) REVERT: G 6 LYS cc_start: 0.8890 (mtpp) cc_final: 0.8667 (mtpp) REVERT: G 42 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7511 (mtm180) REVERT: G 63 LYS cc_start: 0.8955 (mtpt) cc_final: 0.8640 (mtpt) REVERT: I 41 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7355 (pm20) REVERT: L 16 GLU cc_start: 0.8661 (mp0) cc_final: 0.8441 (mp0) REVERT: L 24 GLU cc_start: 0.8190 (mp0) cc_final: 0.7891 (mp0) REVERT: L 60 ASN cc_start: 0.8411 (t0) cc_final: 0.8048 (t0) REVERT: L 62 GLN cc_start: 0.8532 (mp10) cc_final: 0.8195 (mp10) REVERT: L 64 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8037 (tm-30) REVERT: M 14 ARG cc_start: 0.8290 (mtm110) cc_final: 0.7915 (ttp80) REVERT: N 11 TYR cc_start: 0.8813 (t80) cc_final: 0.8603 (t80) REVERT: N 14 ARG cc_start: 0.8484 (tpp80) cc_final: 0.8129 (tpp80) REVERT: O 95 TYR cc_start: 0.7818 (t80) cc_final: 0.6931 (t80) REVERT: P 49 SER cc_start: 0.9341 (m) cc_final: 0.8800 (p) outliers start: 30 outliers final: 12 residues processed: 395 average time/residue: 0.1260 time to fit residues: 71.9650 Evaluate side-chains 368 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 350 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain K residue 25 ASN Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain P residue 55 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 51 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 114 optimal weight: 0.0470 chunk 139 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 107 optimal weight: 0.0270 chunk 131 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 40 GLN ** J 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 GLN A 187 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.091989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.072216 restraints weight = 30553.099| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.71 r_work: 0.2937 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14312 Z= 0.124 Angle : 0.605 16.701 19395 Z= 0.310 Chirality : 0.042 0.173 2255 Planarity : 0.004 0.047 2497 Dihedral : 4.629 53.278 1914 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.99 % Allowed : 22.19 % Favored : 75.82 % 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 (0.21), residues: 1729 helix: 0.40 (0.17), residues: 1032 sheet: -1.30 (0.36), residues: 196 loop : 0.66 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 54 TYR 0.037 0.001 TYR P 95 PHE 0.015 0.001 PHE A 107 TRP 0.007 0.001 TRP O 56 HIS 0.007 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00292 (14312) covalent geometry : angle 0.60469 (19395) hydrogen bonds : bond 0.03145 ( 728) hydrogen bonds : angle 4.67107 ( 2061) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 375 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.7998 (tm-30) REVERT: H 21 ASP cc_start: 0.8399 (m-30) cc_final: 0.7933 (m-30) REVERT: H 41 GLN cc_start: 0.8900 (mp10) cc_final: 0.8185 (mp10) REVERT: H 60 ASN cc_start: 0.8927 (t0) cc_final: 0.8513 (p0) REVERT: F 54 ARG cc_start: 0.7069 (mmt-90) cc_final: 0.6609 (mmt-90) REVERT: J 18 GLU cc_start: 0.8843 (mp0) cc_final: 0.8475 (mp0) REVERT: J 21 ASP cc_start: 0.8125 (m-30) cc_final: 0.7091 (m-30) REVERT: K 41 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7143 (mp10) REVERT: K 51 GLU cc_start: 0.8332 (tp30) cc_final: 0.7833 (mm-30) REVERT: K 62 GLN cc_start: 0.7802 (pp30) cc_final: 0.7464 (pp30) REVERT: A 138 CYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8598 (m) REVERT: B 8 ASP cc_start: 0.8329 (t70) cc_final: 0.8010 (t0) REVERT: B 95 MET cc_start: 0.8937 (mmt) cc_final: 0.8577 (mmp) REVERT: B 101 ASP cc_start: 0.7963 (t0) cc_final: 0.7664 (t0) REVERT: B 127 ASP cc_start: 0.8328 (m-30) cc_final: 0.8070 (m-30) REVERT: C 24 MET cc_start: 0.8932 (ptp) cc_final: 0.8701 (ptm) REVERT: C 158 ASN cc_start: 0.8716 (p0) cc_final: 0.8495 (p0) REVERT: D 13 TYR cc_start: 0.8801 (t80) cc_final: 0.8599 (t80) REVERT: D 41 GLU cc_start: 0.8388 (tm-30) cc_final: 0.8104 (tm-30) REVERT: D 60 GLU cc_start: 0.8332 (tt0) cc_final: 0.7995 (tt0) REVERT: E 2 GLN cc_start: 0.8271 (tm-30) cc_final: 0.7984 (tm-30) REVERT: E 33 LYS cc_start: 0.7963 (mtmt) cc_final: 0.7408 (pttm) REVERT: E 51 GLU cc_start: 0.8498 (tp30) cc_final: 0.8091 (tp30) REVERT: G 6 LYS cc_start: 0.8914 (mtpp) cc_final: 0.8697 (mtpp) REVERT: G 22 THR cc_start: 0.9172 (p) cc_final: 0.8953 (t) REVERT: G 42 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7562 (mtm180) REVERT: I 41 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7451 (pm20) REVERT: L 24 GLU cc_start: 0.8220 (mp0) cc_final: 0.7861 (mp0) REVERT: L 60 ASN cc_start: 0.8405 (t0) cc_final: 0.8031 (t0) REVERT: L 62 GLN cc_start: 0.8474 (mp10) cc_final: 0.8165 (mp10) REVERT: L 64 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8011 (tm-30) REVERT: M 14 ARG cc_start: 0.8310 (mtm110) cc_final: 0.7961 (ttp80) REVERT: N 1 MET cc_start: 0.6282 (tpp) cc_final: 0.5594 (tpp) REVERT: N 11 TYR cc_start: 0.8813 (t80) cc_final: 0.8578 (t80) REVERT: O 95 TYR cc_start: 0.7699 (t80) cc_final: 0.6923 (t80) REVERT: P 49 SER cc_start: 0.9349 (m) cc_final: 0.8813 (p) outliers start: 31 outliers final: 14 residues processed: 395 average time/residue: 0.1249 time to fit residues: 71.3902 Evaluate side-chains 371 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 352 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain P residue 17 SER Chi-restraints excluded: chain P residue 55 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 121 optimal weight: 6.9990 chunk 137 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 151 optimal weight: 0.8980 chunk 167 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 overall best weight: 1.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 40 GLN ** O 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.090314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.070234 restraints weight = 30778.556| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.72 r_work: 0.2927 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14312 Z= 0.176 Angle : 0.637 14.506 19395 Z= 0.324 Chirality : 0.044 0.202 2255 Planarity : 0.004 0.047 2497 Dihedral : 4.625 53.509 1914 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.93 % Allowed : 23.02 % Favored : 75.05 % 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 (0.21), residues: 1729 helix: 0.41 (0.17), residues: 1028 sheet: -1.23 (0.37), residues: 196 loop : 0.60 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 54 TYR 0.037 0.001 TYR N 95 PHE 0.026 0.001 PHE K 45 TRP 0.008 0.001 TRP A 177 HIS 0.007 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00423 (14312) covalent geometry : angle 0.63675 (19395) hydrogen bonds : bond 0.03257 ( 728) hydrogen bonds : angle 4.68361 ( 2061) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 356 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.7997 (tm-30) REVERT: H 21 ASP cc_start: 0.8455 (m-30) cc_final: 0.7981 (m-30) REVERT: H 41 GLN cc_start: 0.8896 (mp10) cc_final: 0.8179 (mp10) REVERT: F 54 ARG cc_start: 0.7096 (mmt-90) cc_final: 0.6678 (mmt-90) REVERT: J 18 GLU cc_start: 0.8860 (mp0) cc_final: 0.8463 (mp0) REVERT: J 21 ASP cc_start: 0.8167 (m-30) cc_final: 0.7138 (m-30) REVERT: J 51 GLU cc_start: 0.8019 (tt0) cc_final: 0.7706 (mm-30) REVERT: K 14 THR cc_start: 0.8144 (m) cc_final: 0.7715 (p) REVERT: K 41 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.7244 (mp10) REVERT: K 62 GLN cc_start: 0.7883 (pp30) cc_final: 0.7646 (pp30) REVERT: B 8 ASP cc_start: 0.8384 (t70) cc_final: 0.8077 (t0) REVERT: B 95 MET cc_start: 0.8850 (mmt) cc_final: 0.8475 (mmp) REVERT: B 101 ASP cc_start: 0.8027 (t0) cc_final: 0.7707 (t0) REVERT: B 127 ASP cc_start: 0.8260 (m-30) cc_final: 0.7979 (m-30) REVERT: C 158 ASN cc_start: 0.8750 (p0) cc_final: 0.8531 (p0) REVERT: D 41 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8187 (tm-30) REVERT: D 60 GLU cc_start: 0.8355 (tt0) cc_final: 0.8064 (tt0) REVERT: E 33 LYS cc_start: 0.7929 (mtmt) cc_final: 0.7390 (pttm) REVERT: E 51 GLU cc_start: 0.8503 (tp30) cc_final: 0.8088 (tp30) REVERT: G 1 MET cc_start: 0.7533 (ttp) cc_final: 0.7131 (ttp) REVERT: G 6 LYS cc_start: 0.8950 (mtpp) cc_final: 0.8750 (mtpp) REVERT: I 41 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7489 (pm20) REVERT: L 24 GLU cc_start: 0.8209 (mp0) cc_final: 0.7763 (mp0) REVERT: L 60 ASN cc_start: 0.8384 (t0) cc_final: 0.8005 (t0) REVERT: L 62 GLN cc_start: 0.8471 (mp10) cc_final: 0.8153 (mp10) REVERT: L 64 GLU cc_start: 0.8421 (tm-30) cc_final: 0.7627 (tm-30) REVERT: M 14 ARG cc_start: 0.8312 (mtm110) cc_final: 0.7966 (ttp80) REVERT: N 11 TYR cc_start: 0.8852 (t80) cc_final: 0.8610 (t80) REVERT: O 1 MET cc_start: 0.7510 (tpp) cc_final: 0.7265 (mmm) REVERT: O 95 TYR cc_start: 0.7844 (t80) cc_final: 0.6973 (t80) REVERT: P 49 SER cc_start: 0.9383 (m) cc_final: 0.8812 (p) outliers start: 30 outliers final: 19 residues processed: 378 average time/residue: 0.1260 time to fit residues: 68.9499 Evaluate side-chains 360 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 338 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain K residue 25 ASN Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain P residue 17 SER Chi-restraints excluded: chain P residue 55 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 130 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 113 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 40 GLN A 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.091271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.071238 restraints weight = 30634.653| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.73 r_work: 0.2958 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14312 Z= 0.135 Angle : 0.617 13.015 19395 Z= 0.317 Chirality : 0.043 0.175 2255 Planarity : 0.004 0.044 2497 Dihedral : 4.599 54.277 1914 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.12 % Allowed : 23.02 % Favored : 74.86 % 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 (0.21), residues: 1729 helix: 0.47 (0.17), residues: 1028 sheet: -1.17 (0.37), residues: 196 loop : 0.62 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 54 TYR 0.036 0.001 TYR P 95 PHE 0.019 0.001 PHE K 45 TRP 0.008 0.001 TRP O 56 HIS 0.007 0.001 HIS C 111 Details of bonding type rmsd covalent geometry : bond 0.00320 (14312) covalent geometry : angle 0.61732 (19395) hydrogen bonds : bond 0.03088 ( 728) hydrogen bonds : angle 4.63110 ( 2061) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 364 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.7982 (tm-30) REVERT: H 21 ASP cc_start: 0.8428 (m-30) cc_final: 0.7966 (m-30) REVERT: H 41 GLN cc_start: 0.8885 (mp10) cc_final: 0.8144 (mp10) REVERT: F 54 ARG cc_start: 0.7257 (mmt-90) cc_final: 0.6846 (mmt-90) REVERT: J 18 GLU cc_start: 0.8893 (mp0) cc_final: 0.8482 (mp0) REVERT: J 21 ASP cc_start: 0.8180 (m-30) cc_final: 0.7144 (m-30) REVERT: J 51 GLU cc_start: 0.7981 (tt0) cc_final: 0.7715 (mm-30) REVERT: K 14 THR cc_start: 0.8273 (m) cc_final: 0.7898 (p) REVERT: K 41 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.7130 (mp10) REVERT: B 8 ASP cc_start: 0.8351 (t70) cc_final: 0.8055 (t0) REVERT: B 68 LYS cc_start: 0.8897 (ptpp) cc_final: 0.8679 (ptpp) REVERT: B 95 MET cc_start: 0.8853 (mmt) cc_final: 0.8516 (mmp) REVERT: B 101 ASP cc_start: 0.8037 (t0) cc_final: 0.7720 (t0) REVERT: B 127 ASP cc_start: 0.8386 (m-30) cc_final: 0.8121 (m-30) REVERT: C 158 ASN cc_start: 0.8742 (p0) cc_final: 0.8540 (p0) REVERT: D 41 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8133 (tm-30) REVERT: E 33 LYS cc_start: 0.7943 (mttt) cc_final: 0.7392 (pttm) REVERT: E 51 GLU cc_start: 0.8508 (tp30) cc_final: 0.8129 (tp30) REVERT: G 1 MET cc_start: 0.7570 (ttp) cc_final: 0.7271 (ttp) REVERT: G 24 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8559 (mm-30) REVERT: I 2 GLN cc_start: 0.8339 (tp40) cc_final: 0.7901 (tp40) REVERT: I 41 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7505 (pm20) REVERT: I 62 GLN cc_start: 0.8075 (pp30) cc_final: 0.7600 (pp30) REVERT: L 24 GLU cc_start: 0.8102 (mp0) cc_final: 0.7804 (mp0) REVERT: L 60 ASN cc_start: 0.8371 (t0) cc_final: 0.7968 (t0) REVERT: L 62 GLN cc_start: 0.8478 (mp10) cc_final: 0.8170 (mp10) REVERT: L 64 GLU cc_start: 0.8362 (tm-30) cc_final: 0.7571 (tm-30) REVERT: M 14 ARG cc_start: 0.8310 (mtm110) cc_final: 0.7967 (ttp80) REVERT: N 11 TYR cc_start: 0.8837 (t80) cc_final: 0.8634 (t80) REVERT: O 93 GLN cc_start: 0.9051 (pp30) cc_final: 0.8809 (pp30) REVERT: O 95 TYR cc_start: 0.7814 (t80) cc_final: 0.6949 (t80) REVERT: P 49 SER cc_start: 0.9367 (m) cc_final: 0.8830 (p) outliers start: 33 outliers final: 25 residues processed: 386 average time/residue: 0.1264 time to fit residues: 70.9647 Evaluate side-chains 374 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 346 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain K residue 25 ASN Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 72 ARG Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain P residue 17 SER Chi-restraints excluded: chain P residue 55 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 129 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 134 optimal weight: 0.5980 chunk 141 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 40 GLN ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.089437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.069344 restraints weight = 30672.764| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.74 r_work: 0.2884 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14312 Z= 0.196 Angle : 0.660 12.979 19395 Z= 0.338 Chirality : 0.045 0.183 2255 Planarity : 0.004 0.046 2497 Dihedral : 4.659 53.661 1914 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.32 % Allowed : 22.89 % Favored : 74.79 % 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: 0.27 (0.21), residues: 1729 helix: 0.42 (0.17), residues: 1034 sheet: -1.09 (0.37), residues: 196 loop : 0.65 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 54 TYR 0.034 0.002 TYR P 95 PHE 0.016 0.001 PHE K 45 TRP 0.008 0.001 TRP A 177 HIS 0.007 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00468 (14312) covalent geometry : angle 0.66035 (19395) hydrogen bonds : bond 0.03302 ( 728) hydrogen bonds : angle 4.69696 ( 2061) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 349 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 16 GLU cc_start: 0.7967 (tp30) cc_final: 0.7532 (tp30) REVERT: H 18 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.7937 (tm-30) REVERT: H 21 ASP cc_start: 0.8479 (m-30) cc_final: 0.7966 (m-30) REVERT: H 41 GLN cc_start: 0.8865 (mp10) cc_final: 0.8070 (mp10) REVERT: F 21 ASP cc_start: 0.8542 (t0) cc_final: 0.8097 (t70) REVERT: F 50 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8093 (mp) REVERT: F 54 ARG cc_start: 0.7310 (mmt-90) cc_final: 0.6868 (mmt-90) REVERT: J 18 GLU cc_start: 0.8857 (mp0) cc_final: 0.8440 (mp0) REVERT: J 21 ASP cc_start: 0.8185 (m-30) cc_final: 0.7093 (m-30) REVERT: K 14 THR cc_start: 0.8257 (m) cc_final: 0.7932 (p) REVERT: K 41 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7105 (mp10) REVERT: B 8 ASP cc_start: 0.8357 (t70) cc_final: 0.8054 (t0) REVERT: B 68 LYS cc_start: 0.8963 (ptpp) cc_final: 0.8720 (ptpp) REVERT: B 101 ASP cc_start: 0.8138 (t0) cc_final: 0.7752 (t0) REVERT: B 127 ASP cc_start: 0.8379 (m-30) cc_final: 0.8110 (m-30) REVERT: D 41 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8228 (tm-30) REVERT: E 33 LYS cc_start: 0.8042 (mttt) cc_final: 0.7426 (pttm) REVERT: E 51 GLU cc_start: 0.8604 (tp30) cc_final: 0.8305 (tp30) REVERT: G 1 MET cc_start: 0.7595 (ttp) cc_final: 0.7356 (ttp) REVERT: G 24 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8546 (mm-30) REVERT: G 42 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7382 (mtm180) REVERT: I 41 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7325 (pm20) REVERT: L 24 GLU cc_start: 0.8168 (mp0) cc_final: 0.7862 (mp0) REVERT: L 60 ASN cc_start: 0.8415 (t0) cc_final: 0.7994 (t0) REVERT: L 62 GLN cc_start: 0.8508 (mp10) cc_final: 0.8168 (mp10) REVERT: L 64 GLU cc_start: 0.8423 (tm-30) cc_final: 0.7634 (tm-30) REVERT: M 14 ARG cc_start: 0.8357 (mtm110) cc_final: 0.7993 (ttp80) REVERT: M 93 GLN cc_start: 0.8541 (pp30) cc_final: 0.8310 (pp30) REVERT: N 11 TYR cc_start: 0.8857 (t80) cc_final: 0.8611 (t80) REVERT: O 40 ASP cc_start: 0.8701 (m-30) cc_final: 0.8480 (m-30) REVERT: O 95 TYR cc_start: 0.7965 (t80) cc_final: 0.7033 (t80) REVERT: P 49 SER cc_start: 0.9362 (m) cc_final: 0.8773 (p) outliers start: 36 outliers final: 27 residues processed: 374 average time/residue: 0.1201 time to fit residues: 65.6032 Evaluate side-chains 373 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 341 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain E residue 4 PHE Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 72 ARG Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain P residue 17 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 60 optimal weight: 0.0040 chunk 99 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 40 GLN J 41 GLN C 158 ASN ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.092005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.071968 restraints weight = 30583.330| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.74 r_work: 0.2957 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14312 Z= 0.125 Angle : 0.626 12.012 19395 Z= 0.325 Chirality : 0.042 0.174 2255 Planarity : 0.004 0.044 2497 Dihedral : 4.590 54.708 1914 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.06 % Allowed : 23.60 % Favored : 74.34 % 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: 0.37 (0.21), residues: 1729 helix: 0.53 (0.17), residues: 1030 sheet: -1.03 (0.37), residues: 198 loop : 0.59 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 54 TYR 0.033 0.001 TYR P 95 PHE 0.014 0.001 PHE A 107 TRP 0.009 0.001 TRP N 56 HIS 0.006 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00292 (14312) covalent geometry : angle 0.62635 (19395) hydrogen bonds : bond 0.02978 ( 728) hydrogen bonds : angle 4.59205 ( 2061) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 361 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.7967 (tm-30) REVERT: H 21 ASP cc_start: 0.8452 (m-30) cc_final: 0.7965 (m-30) REVERT: H 41 GLN cc_start: 0.8881 (mp10) cc_final: 0.8094 (mp10) REVERT: H 54 ARG cc_start: 0.8763 (mmt-90) cc_final: 0.8316 (mmt-90) REVERT: F 21 ASP cc_start: 0.8570 (t0) cc_final: 0.8034 (t70) REVERT: F 50 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7972 (mp) REVERT: F 54 ARG cc_start: 0.7204 (mmt-90) cc_final: 0.6813 (mmt-90) REVERT: J 18 GLU cc_start: 0.8843 (mp0) cc_final: 0.8278 (mp0) REVERT: J 21 ASP cc_start: 0.8143 (m-30) cc_final: 0.7010 (m-30) REVERT: K 14 THR cc_start: 0.8176 (m) cc_final: 0.7845 (p) REVERT: K 41 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7129 (mp10) REVERT: B 8 ASP cc_start: 0.8365 (t70) cc_final: 0.8072 (t0) REVERT: B 68 LYS cc_start: 0.8895 (ptpp) cc_final: 0.8654 (ptpp) REVERT: B 101 ASP cc_start: 0.8023 (t0) cc_final: 0.7695 (t0) REVERT: B 127 ASP cc_start: 0.8299 (m-30) cc_final: 0.8053 (m-30) REVERT: D 41 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8119 (tm-30) REVERT: E 51 GLU cc_start: 0.8533 (tp30) cc_final: 0.8198 (tp30) REVERT: G 24 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8552 (mm-30) REVERT: G 42 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7546 (mtm180) REVERT: I 41 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7489 (pm20) REVERT: L 24 GLU cc_start: 0.8093 (mp0) cc_final: 0.7809 (mp0) REVERT: L 60 ASN cc_start: 0.8414 (t0) cc_final: 0.8029 (t0) REVERT: M 14 ARG cc_start: 0.8273 (mtm110) cc_final: 0.7916 (ttp80) REVERT: O 95 TYR cc_start: 0.7729 (t80) cc_final: 0.6924 (t80) REVERT: P 49 SER cc_start: 0.9341 (m) cc_final: 0.8760 (p) outliers start: 32 outliers final: 20 residues processed: 382 average time/residue: 0.1235 time to fit residues: 68.2735 Evaluate side-chains 364 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 339 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 72 ARG Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain N residue 93 GLN Chi-restraints excluded: chain P residue 17 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 86 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 157 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 0.0000 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 40 GLN ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.091647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.072285 restraints weight = 30393.988| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.65 r_work: 0.2947 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.175 14312 Z= 0.191 Angle : 0.835 59.200 19395 Z= 0.474 Chirality : 0.045 0.845 2255 Planarity : 0.004 0.091 2497 Dihedral : 4.613 54.769 1914 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.93 % Allowed : 24.63 % Favored : 73.44 % Cbeta Deviations : 0.06 % 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: 0.38 (0.21), residues: 1729 helix: 0.53 (0.17), residues: 1036 sheet: -1.02 (0.37), residues: 198 loop : 0.61 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG O 65 TYR 0.032 0.001 TYR P 95 PHE 0.060 0.002 PHE L 4 TRP 0.009 0.001 TRP N 56 HIS 0.005 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00416 (14312) covalent geometry : angle 0.83468 (19395) hydrogen bonds : bond 0.02983 ( 728) hydrogen bonds : angle 4.59433 ( 2061) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3224.77 seconds wall clock time: 56 minutes 10.71 seconds (3370.71 seconds total)