Starting phenix.real_space_refine on Thu Jul 31 22:54:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dni_30784/07_2025/7dni_30784.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dni_30784/07_2025/7dni_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_30784/07_2025/7dni_30784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dni_30784/07_2025/7dni_30784.map" model { file = "/net/cci-nas-00/data/ceres_data/7dni_30784/07_2025/7dni_30784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dni_30784/07_2025/7dni_30784.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP: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: 8.79, per 1000 atoms: 0.62 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: 3.30 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.41 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: 4.07 Time building geometry restraints manager: 3.92 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.630 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.570 ------------------------------------------------------------------------------- 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 : 14.42 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.011 0.002 TRP D 177 HIS 0.008 0.002 HIS A 111 PHE 0.016 0.002 PHE C 107 TYR 0.034 0.002 TYR O 95 ARG 0.007 0.001 ARG E 42 Details of bonding type rmsd hydrogen bonds : bond 0.25785 ( 728) hydrogen bonds : angle 9.79191 ( 2061) covalent geometry : bond 0.00900 (14312) covalent geometry : angle 0.84203 (19395) *********************** 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 : 1.782 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: 0.7599 (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: 0.8498 (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: 0.8737 (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: 0.3411 time to fit residues: 193.3245 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 : 2.318 ------------------------------------------------------------------------------- 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 141 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 P 15 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.090098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.070496 restraints weight = 30461.944| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.59 r_work: 0.2903 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14312 Z= 0.163 Angle : 0.677 9.723 19395 Z= 0.356 Chirality : 0.044 0.205 2255 Planarity : 0.005 0.058 2497 Dihedral : 5.527 55.933 1922 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.35 % Allowed : 11.45 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.20), residues: 1729 helix: -0.62 (0.15), residues: 1044 sheet: -1.79 (0.35), residues: 198 loop : 0.68 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 75 HIS 0.005 0.001 HIS A 72 PHE 0.018 0.001 PHE A 107 TYR 0.017 0.001 TYR B 13 ARG 0.009 0.001 ARG N 52 Details of bonding type rmsd hydrogen bonds : bond 0.05082 ( 728) hydrogen bonds : angle 5.78834 ( 2061) covalent geometry : bond 0.00362 (14312) covalent geometry : angle 0.67728 (19395) *********************** 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: 21 poor density : 396 time to evaluate : 1.760 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: 0.8718 (OUTLIER) cc_final: 0.8073 (tm-30) REVERT: H 21 ASP cc_start: 0.8439 (m-30) cc_final: 0.7886 (m-30) REVERT: H 60 ASN cc_start: 0.9039 (t0) cc_final: 0.8765 (p0) REVERT: F 25 ASN cc_start: 0.8528 (t0) cc_final: 0.8212 (t0) REVERT: F 40 GLN cc_start: 0.8162 (mm-40) cc_final: 0.7913 (mm-40) REVERT: F 41 GLN cc_start: 0.7624 (mt0) cc_final: 0.7412 (mt0) REVERT: F 63 LYS cc_start: 0.9085 (ptpt) cc_final: 0.8873 (pttp) REVERT: J 18 GLU cc_start: 0.8725 (mp0) cc_final: 0.8211 (mp0) REVERT: J 31 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8576 (tm-30) REVERT: K 62 GLN cc_start: 0.7581 (pp30) cc_final: 0.7294 (pp30) REVERT: A 112 ASP cc_start: 0.8430 (m-30) cc_final: 0.8203 (m-30) REVERT: B 8 ASP cc_start: 0.8303 (t70) cc_final: 0.7929 (t0) REVERT: B 101 ASP cc_start: 0.8009 (t0) cc_final: 0.7544 (t0) REVERT: B 127 ASP cc_start: 0.8273 (m-30) cc_final: 0.8025 (m-30) REVERT: B 148 ASP cc_start: 0.8487 (m-30) cc_final: 0.8182 (m-30) REVERT: B 170 ARG cc_start: 0.8593 (mmt90) cc_final: 0.8145 (mmm-85) REVERT: D 41 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8169 (tm-30) REVERT: D 112 ASP cc_start: 0.8647 (t0) cc_final: 0.8373 (t0) REVERT: E 4 PHE cc_start: 0.7868 (m-80) cc_final: 0.7557 (m-10) REVERT: E 48 LYS cc_start: 0.9090 (tttp) cc_final: 0.8667 (tptt) REVERT: G 24 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8471 (mm-30) REVERT: G 34 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7350 (mm-30) REVERT: G 42 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7607 (mtm180) REVERT: L 24 GLU cc_start: 0.8115 (mp0) cc_final: 0.7785 (mp0) REVERT: L 64 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8086 (tm-30) REVERT: N 86 ASP cc_start: 0.8472 (p0) cc_final: 0.8242 (p0) REVERT: N 93 GLN cc_start: 0.8578 (pm20) cc_final: 0.8089 (pm20) REVERT: O 93 GLN cc_start: 0.9026 (pp30) cc_final: 0.8785 (pp30) REVERT: P 6 ASP cc_start: 0.8419 (t0) cc_final: 0.8158 (t0) outliers start: 21 outliers final: 10 residues processed: 408 average time/residue: 0.2911 time to fit residues: 170.2053 Evaluate side-chains 353 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 341 time to evaluate : 1.676 ------------------------------------------------------------------------------- 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 9 THR 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 82 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 162 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 114 optimal weight: 0.0370 overall best weight: 1.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 49 GLN A 150 ASN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.089412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.069748 restraints weight = 30435.357| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.68 r_work: 0.2886 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14312 Z= 0.169 Angle : 0.632 7.816 19395 Z= 0.327 Chirality : 0.044 0.196 2255 Planarity : 0.004 0.055 2497 Dihedral : 4.978 48.884 1914 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.32 % Allowed : 14.34 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.20), residues: 1729 helix: -0.23 (0.16), residues: 1028 sheet: -1.62 (0.35), residues: 193 loop : 0.63 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 56 HIS 0.006 0.001 HIS A 111 PHE 0.022 0.001 PHE P 3 TYR 0.029 0.002 TYR P 95 ARG 0.007 0.000 ARG O 41 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 728) hydrogen bonds : angle 5.28202 ( 2061) covalent geometry : bond 0.00401 (14312) covalent geometry : angle 0.63203 (19395) *********************** 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 404 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 368 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.7905 (tm-30) REVERT: H 21 ASP cc_start: 0.8436 (m-30) cc_final: 0.7764 (m-30) REVERT: H 31 GLN cc_start: 0.8798 (tp40) cc_final: 0.8308 (tp40) REVERT: H 41 GLN cc_start: 0.8932 (mp10) cc_final: 0.8580 (mp10) REVERT: H 60 ASN cc_start: 0.9070 (t0) cc_final: 0.8639 (p0) REVERT: F 25 ASN cc_start: 0.8496 (t0) cc_final: 0.8246 (t0) REVERT: F 41 GLN cc_start: 0.7604 (mt0) cc_final: 0.7346 (mt0) REVERT: F 63 LYS cc_start: 0.9027 (ptpt) cc_final: 0.8806 (pttp) REVERT: J 18 GLU cc_start: 0.8851 (mp0) cc_final: 0.8476 (mp0) REVERT: J 31 GLN cc_start: 0.8939 (tm-30) cc_final: 0.8601 (tm-30) REVERT: K 11 LYS cc_start: 0.8354 (tmtt) cc_final: 0.8083 (tmtt) REVERT: B 8 ASP cc_start: 0.8307 (t70) cc_final: 0.7966 (t0) REVERT: B 101 ASP cc_start: 0.8116 (t0) cc_final: 0.7767 (t0) REVERT: B 118 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8698 (tt) REVERT: B 127 ASP cc_start: 0.8366 (m-30) cc_final: 0.8105 (m-30) REVERT: C 112 ASP cc_start: 0.8994 (m-30) cc_final: 0.8713 (m-30) REVERT: D 41 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8158 (tm-30) REVERT: D 112 ASP cc_start: 0.8702 (t0) cc_final: 0.8421 (t0) REVERT: D 137 LYS cc_start: 0.9246 (tppp) cc_final: 0.8929 (tppt) REVERT: E 4 PHE cc_start: 0.7740 (m-80) cc_final: 0.7531 (m-80) REVERT: E 48 LYS cc_start: 0.9101 (tttp) cc_final: 0.8715 (tptt) REVERT: G 2 GLN cc_start: 0.8043 (tm-30) cc_final: 0.7661 (tm-30) REVERT: G 42 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7556 (mtm180) REVERT: I 41 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7381 (pm20) REVERT: L 64 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8137 (tm-30) REVERT: M 14 ARG cc_start: 0.8391 (mtm110) cc_final: 0.8150 (ttp-110) REVERT: N 14 ARG cc_start: 0.8520 (tpp80) cc_final: 0.8236 (tpp80) REVERT: O 93 GLN cc_start: 0.9084 (pp30) cc_final: 0.8819 (pp30) REVERT: O 95 TYR cc_start: 0.7836 (t80) cc_final: 0.6893 (t80) REVERT: P 6 ASP cc_start: 0.8400 (t0) cc_final: 0.8160 (t0) REVERT: P 49 SER cc_start: 0.9388 (m) cc_final: 0.8732 (p) REVERT: P 95 TYR cc_start: 0.5696 (t80) cc_final: 0.5016 (t80) outliers start: 36 outliers final: 15 residues processed: 392 average time/residue: 0.2726 time to fit residues: 151.8109 Evaluate side-chains 353 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 334 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 18 GLU 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 118 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 198 THR 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 90 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 119 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 25 ASN K 60 ASN A 47 GLN A 116 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN L 68 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.090826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.070999 restraints weight = 30657.558| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.73 r_work: 0.2924 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14312 Z= 0.129 Angle : 0.593 8.312 19395 Z= 0.311 Chirality : 0.043 0.196 2255 Planarity : 0.004 0.053 2497 Dihedral : 4.828 50.653 1914 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.12 % Allowed : 17.68 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.21), residues: 1729 helix: 0.08 (0.16), residues: 1033 sheet: -1.61 (0.35), residues: 198 loop : 0.63 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 56 HIS 0.006 0.001 HIS A 111 PHE 0.015 0.001 PHE P 3 TYR 0.024 0.001 TYR M 95 ARG 0.007 0.000 ARG H 54 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 728) hydrogen bonds : angle 4.95922 ( 2061) covalent geometry : bond 0.00296 (14312) covalent geometry : angle 0.59331 (19395) *********************** 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 403 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 370 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 16 GLU cc_start: 0.8002 (tp30) cc_final: 0.7585 (tp30) REVERT: H 21 ASP cc_start: 0.8454 (m-30) cc_final: 0.8005 (m-30) REVERT: H 41 GLN cc_start: 0.8912 (mp10) cc_final: 0.8187 (mp10) REVERT: H 60 ASN cc_start: 0.9001 (t0) cc_final: 0.8528 (p0) REVERT: F 41 GLN cc_start: 0.7570 (mt0) cc_final: 0.7340 (mt0) REVERT: F 63 LYS cc_start: 0.8973 (ptpt) cc_final: 0.8733 (pttp) REVERT: J 18 GLU cc_start: 0.8868 (mp0) cc_final: 0.8454 (mp0) REVERT: J 31 GLN cc_start: 0.9001 (tm-30) cc_final: 0.8798 (tp40) REVERT: K 11 LYS cc_start: 0.8303 (tmtt) cc_final: 0.8087 (tmtt) REVERT: K 62 GLN cc_start: 0.7709 (pp30) cc_final: 0.7447 (pp30) REVERT: B 8 ASP cc_start: 0.8286 (t70) cc_final: 0.7950 (t0) REVERT: B 101 ASP cc_start: 0.8162 (t0) cc_final: 0.7776 (t0) REVERT: B 118 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8610 (tt) REVERT: B 127 ASP cc_start: 0.8319 (m-30) cc_final: 0.8056 (m-30) REVERT: B 147 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8429 (tp30) REVERT: C 24 MET cc_start: 0.9114 (mtm) cc_final: 0.8874 (ptp) REVERT: C 112 ASP cc_start: 0.9040 (m-30) cc_final: 0.8696 (m-30) REVERT: C 158 ASN cc_start: 0.8792 (p0) cc_final: 0.8553 (p0) REVERT: D 13 TYR cc_start: 0.8726 (t80) cc_final: 0.8364 (t80) REVERT: D 41 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8136 (tm-30) REVERT: D 112 ASP cc_start: 0.8715 (t0) cc_final: 0.8435 (t0) REVERT: E 48 LYS cc_start: 0.9155 (tttp) cc_final: 0.8769 (tptt) REVERT: G 6 LYS cc_start: 0.8895 (mtpp) cc_final: 0.8640 (mtpp) REVERT: G 42 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7561 (mtm180) REVERT: I 1 MET cc_start: 0.7628 (tpt) cc_final: 0.7130 (tpt) REVERT: I 11 LYS cc_start: 0.8287 (pptt) cc_final: 0.8076 (pptt) REVERT: I 41 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7412 (pm20) REVERT: L 16 GLU cc_start: 0.8647 (mp0) cc_final: 0.8372 (mp0) REVERT: L 24 GLU cc_start: 0.8136 (mp0) cc_final: 0.7804 (mp0) REVERT: L 60 ASN cc_start: 0.8382 (t0) cc_final: 0.8147 (t0) REVERT: L 64 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8145 (tm-30) REVERT: M 14 ARG cc_start: 0.8337 (mtm110) cc_final: 0.7947 (ttp80) REVERT: M 87 GLU cc_start: 0.9057 (tm-30) cc_final: 0.8420 (tm-30) REVERT: N 14 ARG cc_start: 0.8603 (tpp80) cc_final: 0.8258 (tpp80) REVERT: O 93 GLN cc_start: 0.9123 (pp30) cc_final: 0.8830 (pp30) REVERT: O 95 TYR cc_start: 0.7808 (t80) cc_final: 0.7045 (t80) REVERT: P 6 ASP cc_start: 0.8319 (t0) cc_final: 0.8113 (t0) REVERT: P 49 SER cc_start: 0.9378 (m) cc_final: 0.8804 (p) REVERT: P 95 TYR cc_start: 0.6245 (t80) cc_final: 0.6040 (t80) outliers start: 33 outliers final: 14 residues processed: 392 average time/residue: 0.2723 time to fit residues: 152.0533 Evaluate side-chains 350 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 332 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 58 ASP 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 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 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 P residue 10 LYS Chi-restraints excluded: chain P residue 17 SER 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 122 optimal weight: 8.9990 chunk 116 optimal weight: 6.9990 chunk 78 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 153 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 96 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 49 GLN A 47 GLN D 111 HIS ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.091438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.071505 restraints weight = 30727.260| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.74 r_work: 0.2921 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14312 Z= 0.125 Angle : 0.593 7.778 19395 Z= 0.307 Chirality : 0.043 0.172 2255 Planarity : 0.004 0.050 2497 Dihedral : 4.749 52.098 1914 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.38 % Allowed : 20.00 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.21), residues: 1729 helix: 0.23 (0.16), residues: 1032 sheet: -1.51 (0.35), residues: 198 loop : 0.61 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 56 HIS 0.007 0.001 HIS A 111 PHE 0.016 0.001 PHE E 4 TYR 0.021 0.001 TYR P 95 ARG 0.006 0.000 ARG H 54 Details of bonding type rmsd hydrogen bonds : bond 0.03380 ( 728) hydrogen bonds : angle 4.82184 ( 2061) covalent geometry : bond 0.00289 (14312) covalent geometry : angle 0.59325 (19395) *********************** 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 411 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 374 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 21 ASP cc_start: 0.8410 (m-30) cc_final: 0.7980 (m-30) REVERT: H 31 GLN cc_start: 0.8713 (tp40) cc_final: 0.8234 (tp40) REVERT: H 41 GLN cc_start: 0.8886 (mp10) cc_final: 0.8127 (mp10) REVERT: H 60 ASN cc_start: 0.8970 (t0) cc_final: 0.8540 (p0) REVERT: F 41 GLN cc_start: 0.7546 (mt0) cc_final: 0.7332 (mt0) REVERT: F 63 LYS cc_start: 0.8955 (ptpt) cc_final: 0.8694 (pttp) REVERT: J 18 GLU cc_start: 0.8842 (mp0) cc_final: 0.8497 (mp0) REVERT: J 21 ASP cc_start: 0.8134 (m-30) cc_final: 0.7144 (m-30) REVERT: J 31 GLN cc_start: 0.8966 (tm-30) cc_final: 0.8765 (tp40) REVERT: J 51 GLU cc_start: 0.7987 (tt0) cc_final: 0.7584 (mm-30) REVERT: K 51 GLU cc_start: 0.8367 (tp30) cc_final: 0.7934 (mm-30) REVERT: K 62 GLN cc_start: 0.7696 (pp30) cc_final: 0.7377 (pp30) REVERT: A 138 CYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8571 (m) REVERT: A 187 GLN cc_start: 0.8711 (mt0) cc_final: 0.8408 (mt0) REVERT: B 8 ASP cc_start: 0.8333 (t70) cc_final: 0.7998 (t0) REVERT: B 101 ASP cc_start: 0.8049 (t0) cc_final: 0.7759 (t0) REVERT: B 118 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8582 (tt) REVERT: B 127 ASP cc_start: 0.8262 (m-30) cc_final: 0.8024 (m-30) REVERT: B 147 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8506 (tp30) REVERT: C 112 ASP cc_start: 0.9037 (m-30) cc_final: 0.8696 (m-30) REVERT: C 158 ASN cc_start: 0.8782 (p0) cc_final: 0.8528 (p0) REVERT: D 13 TYR cc_start: 0.8785 (t80) cc_final: 0.8500 (t80) REVERT: D 41 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8122 (tm-30) REVERT: D 56 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8048 (mtt) REVERT: D 60 GLU cc_start: 0.8356 (tt0) cc_final: 0.8120 (tt0) REVERT: D 112 ASP cc_start: 0.8660 (t0) cc_final: 0.8383 (t0) REVERT: E 51 GLU cc_start: 0.8485 (tp30) cc_final: 0.7860 (tp30) REVERT: E 52 ASP cc_start: 0.8153 (p0) cc_final: 0.7910 (p0) REVERT: G 6 LYS cc_start: 0.8901 (mtpp) cc_final: 0.8667 (mtpp) REVERT: G 42 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.7562 (mtm180) REVERT: I 1 MET cc_start: 0.7572 (tpt) cc_final: 0.7270 (tpt) REVERT: I 11 LYS cc_start: 0.8372 (pptt) cc_final: 0.8169 (pptt) REVERT: I 41 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7367 (pm20) REVERT: L 16 GLU cc_start: 0.8670 (mp0) cc_final: 0.8437 (mp0) REVERT: L 24 GLU cc_start: 0.8124 (mp0) cc_final: 0.7847 (mp0) REVERT: L 60 ASN cc_start: 0.8413 (t0) cc_final: 0.8051 (t0) REVERT: L 62 GLN cc_start: 0.8504 (mp10) cc_final: 0.8192 (mp10) REVERT: L 64 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8057 (tm-30) REVERT: M 14 ARG cc_start: 0.8293 (mtm110) cc_final: 0.7922 (ttp80) REVERT: M 63 GLN cc_start: 0.8842 (pp30) cc_final: 0.8276 (pp30) REVERT: N 1 MET cc_start: 0.6418 (tpp) cc_final: 0.5716 (tpp) REVERT: N 11 TYR cc_start: 0.8907 (t80) cc_final: 0.8597 (t80) REVERT: O 95 TYR cc_start: 0.7677 (t80) cc_final: 0.6973 (t80) REVERT: P 6 ASP cc_start: 0.8333 (t0) cc_final: 0.8078 (t0) REVERT: P 49 SER cc_start: 0.9372 (m) cc_final: 0.8807 (p) REVERT: P 95 TYR cc_start: 0.6301 (t80) cc_final: 0.6079 (t80) outliers start: 37 outliers final: 18 residues processed: 401 average time/residue: 0.2829 time to fit residues: 163.8724 Evaluate side-chains 374 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 350 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain J residue 20 SER 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 138 CYS Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 118 LEU 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 118 LEU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain G residue 9 THR 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 10 LYS Chi-restraints excluded: chain P residue 17 SER 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 72 optimal weight: 0.9980 chunk 150 optimal weight: 6.9990 chunk 151 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 A 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.088930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.069276 restraints weight = 31256.141| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.62 r_work: 0.2893 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2890 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= 0.207 Angle : 0.637 16.323 19395 Z= 0.326 Chirality : 0.045 0.185 2255 Planarity : 0.004 0.050 2497 Dihedral : 4.734 52.079 1914 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.51 % Allowed : 21.41 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.21), residues: 1729 helix: 0.22 (0.16), residues: 1033 sheet: -1.49 (0.36), residues: 198 loop : 0.65 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 177 HIS 0.008 0.001 HIS A 111 PHE 0.016 0.001 PHE C 107 TYR 0.019 0.001 TYR N 95 ARG 0.007 0.000 ARG H 54 Details of bonding type rmsd hydrogen bonds : bond 0.03543 ( 728) hydrogen bonds : angle 4.83305 ( 2061) covalent geometry : bond 0.00497 (14312) covalent geometry : angle 0.63720 (19395) *********************** 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 394 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 355 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.7975 (tm-30) REVERT: H 21 ASP cc_start: 0.8478 (m-30) cc_final: 0.7984 (m-30) REVERT: H 41 GLN cc_start: 0.8881 (mp10) cc_final: 0.8191 (mp10) REVERT: F 63 LYS cc_start: 0.8991 (ptpt) cc_final: 0.8745 (pttp) REVERT: J 18 GLU cc_start: 0.8852 (mp0) cc_final: 0.8500 (mp0) REVERT: J 21 ASP cc_start: 0.8171 (m-30) cc_final: 0.7185 (m-30) REVERT: J 31 GLN cc_start: 0.8998 (tm-30) cc_final: 0.8585 (tp40) REVERT: K 31 GLN cc_start: 0.8690 (tm-30) cc_final: 0.8478 (tm-30) REVERT: K 62 GLN cc_start: 0.7749 (pp30) cc_final: 0.7478 (pp30) REVERT: A 47 GLN cc_start: 0.8293 (mm-40) cc_final: 0.8031 (mm-40) REVERT: B 8 ASP cc_start: 0.8388 (t70) cc_final: 0.8087 (t0) REVERT: B 101 ASP cc_start: 0.8040 (t0) cc_final: 0.7712 (t0) REVERT: B 118 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8680 (tt) REVERT: B 127 ASP cc_start: 0.8238 (m-30) cc_final: 0.7989 (m-30) REVERT: C 24 MET cc_start: 0.8949 (ptp) cc_final: 0.8728 (ptm) REVERT: C 158 ASN cc_start: 0.8810 (p0) cc_final: 0.8567 (p0) REVERT: D 41 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8201 (tm-30) REVERT: E 33 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.6901 (pttm) REVERT: E 51 GLU cc_start: 0.8514 (tp30) cc_final: 0.8074 (tp30) REVERT: G 6 LYS cc_start: 0.8899 (mtpp) cc_final: 0.8675 (mtpp) REVERT: I 1 MET cc_start: 0.7504 (tpt) cc_final: 0.7277 (tpt) REVERT: I 41 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7347 (pm20) REVERT: L 60 ASN cc_start: 0.8339 (t0) cc_final: 0.7979 (t0) REVERT: L 62 GLN cc_start: 0.8492 (mp10) cc_final: 0.8186 (mp10) REVERT: L 64 GLU cc_start: 0.8390 (tm-30) cc_final: 0.7629 (tm-30) REVERT: M 14 ARG cc_start: 0.8336 (mtm110) cc_final: 0.7992 (ttp80) REVERT: M 63 GLN cc_start: 0.8885 (pp30) cc_final: 0.8649 (pp30) REVERT: O 40 ASP cc_start: 0.8657 (m-30) cc_final: 0.8418 (m-30) REVERT: O 95 TYR cc_start: 0.7767 (t80) cc_final: 0.7029 (t80) REVERT: P 6 ASP cc_start: 0.8336 (t0) cc_final: 0.8058 (t0) REVERT: P 49 SER cc_start: 0.9404 (m) cc_final: 0.8810 (p) REVERT: P 95 TYR cc_start: 0.6397 (t80) cc_final: 0.6075 (t80) outliers start: 39 outliers final: 23 residues processed: 383 average time/residue: 0.2670 time to fit residues: 147.2127 Evaluate side-chains 370 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 343 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 58 ASP 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 B residue 118 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 E residue 4 PHE Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain L residue 12 THR 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 128 optimal weight: 3.9990 chunk 3 optimal weight: 0.2980 chunk 78 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 151 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3420 r_free = 0.3420 target = 0.090994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.071051 restraints weight = 30835.937| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.75 r_work: 0.2930 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14312 Z= 0.132 Angle : 0.611 13.704 19395 Z= 0.314 Chirality : 0.043 0.177 2255 Planarity : 0.004 0.047 2497 Dihedral : 4.663 53.307 1914 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.38 % Allowed : 22.12 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.21), residues: 1729 helix: 0.31 (0.16), residues: 1041 sheet: -1.40 (0.36), residues: 196 loop : 0.54 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 56 HIS 0.006 0.001 HIS C 111 PHE 0.014 0.001 PHE A 107 TYR 0.022 0.001 TYR N 95 ARG 0.008 0.000 ARG H 54 Details of bonding type rmsd hydrogen bonds : bond 0.03239 ( 728) hydrogen bonds : angle 4.71249 ( 2061) covalent geometry : bond 0.00311 (14312) covalent geometry : angle 0.61075 (19395) *********************** 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 405 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 368 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.7955 (tm-30) REVERT: H 21 ASP cc_start: 0.8461 (m-30) cc_final: 0.7945 (m-30) REVERT: H 41 GLN cc_start: 0.8861 (mp10) cc_final: 0.8113 (mp10) REVERT: F 54 ARG cc_start: 0.7587 (mmt-90) cc_final: 0.6899 (mmt-90) REVERT: F 63 LYS cc_start: 0.8934 (ptpt) cc_final: 0.8665 (pttp) REVERT: J 18 GLU cc_start: 0.8850 (mp0) cc_final: 0.8459 (mp0) REVERT: J 21 ASP cc_start: 0.8138 (m-30) cc_final: 0.7107 (m-30) REVERT: J 31 GLN cc_start: 0.9007 (tm-30) cc_final: 0.8581 (tp40) REVERT: J 51 GLU cc_start: 0.7990 (tt0) cc_final: 0.7633 (mm-30) REVERT: K 41 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7169 (mp10) REVERT: B 8 ASP cc_start: 0.8390 (t70) cc_final: 0.8087 (t0) REVERT: B 101 ASP cc_start: 0.8067 (t0) cc_final: 0.7719 (t0) REVERT: B 118 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8587 (tt) REVERT: B 127 ASP cc_start: 0.8311 (m-30) cc_final: 0.8088 (m-30) REVERT: B 148 ASP cc_start: 0.8550 (m-30) cc_final: 0.8048 (m-30) REVERT: B 170 ARG cc_start: 0.8622 (mmt90) cc_final: 0.8307 (mmt90) REVERT: C 158 ASN cc_start: 0.8757 (p0) cc_final: 0.8541 (p0) REVERT: D 41 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8158 (tm-30) REVERT: E 33 LYS cc_start: 0.7404 (ptpt) cc_final: 0.6941 (pttm) REVERT: E 51 GLU cc_start: 0.8526 (tp30) cc_final: 0.8082 (tp30) REVERT: G 2 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8215 (pp30) REVERT: G 42 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.7537 (mtm180) REVERT: I 1 MET cc_start: 0.7582 (tpt) cc_final: 0.7239 (tpt) REVERT: I 41 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7489 (pm20) REVERT: L 24 GLU cc_start: 0.8184 (mp0) cc_final: 0.7920 (mp0) REVERT: L 60 ASN cc_start: 0.8415 (t0) cc_final: 0.8030 (t0) REVERT: L 62 GLN cc_start: 0.8487 (mp10) cc_final: 0.8158 (mp10) REVERT: L 64 GLU cc_start: 0.8392 (tm-30) cc_final: 0.7519 (tm-30) REVERT: M 14 ARG cc_start: 0.8298 (mtm110) cc_final: 0.7959 (ttp80) REVERT: M 63 GLN cc_start: 0.8847 (pp30) cc_final: 0.8337 (pp30) REVERT: N 1 MET cc_start: 0.6548 (tpp) cc_final: 0.5827 (tpp) REVERT: O 95 TYR cc_start: 0.7754 (t80) cc_final: 0.7056 (t80) REVERT: P 49 SER cc_start: 0.9379 (m) cc_final: 0.8797 (p) REVERT: P 95 TYR cc_start: 0.6341 (t80) cc_final: 0.5980 (t80) outliers start: 37 outliers final: 18 residues processed: 394 average time/residue: 0.3878 time to fit residues: 225.2415 Evaluate side-chains 368 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 344 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 73 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 B residue 16 SER Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 118 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 D residue 130 LEU Chi-restraints excluded: chain G residue 2 GLN Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 52 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 21 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 152 optimal weight: 0.1980 chunk 130 optimal weight: 9.9990 chunk 142 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 40 GLN K 2 GLN D 10 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.090886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.070904 restraints weight = 30664.181| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.71 r_work: 0.2908 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14312 Z= 0.144 Angle : 0.631 12.712 19395 Z= 0.322 Chirality : 0.043 0.190 2255 Planarity : 0.004 0.045 2497 Dihedral : 4.623 53.760 1914 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.25 % Allowed : 23.02 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.21), residues: 1729 helix: 0.44 (0.17), residues: 1033 sheet: -1.31 (0.36), residues: 196 loop : 0.64 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 56 HIS 0.007 0.001 HIS A 111 PHE 0.014 0.001 PHE A 107 TYR 0.021 0.001 TYR N 95 ARG 0.008 0.000 ARG O 41 Details of bonding type rmsd hydrogen bonds : bond 0.03175 ( 728) hydrogen bonds : angle 4.69467 ( 2061) covalent geometry : bond 0.00342 (14312) covalent geometry : angle 0.63082 (19395) *********************** 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 392 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 357 time to evaluate : 2.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8004 (tm-30) REVERT: H 21 ASP cc_start: 0.8461 (m-30) cc_final: 0.7997 (m-30) REVERT: H 41 GLN cc_start: 0.8862 (mp10) cc_final: 0.8118 (mp10) REVERT: F 54 ARG cc_start: 0.7398 (mmt-90) cc_final: 0.6864 (mmt-90) REVERT: F 63 LYS cc_start: 0.8900 (ptpt) cc_final: 0.8637 (pttp) REVERT: J 18 GLU cc_start: 0.8844 (mp0) cc_final: 0.8464 (mp0) REVERT: J 21 ASP cc_start: 0.8153 (m-30) cc_final: 0.7121 (m-30) REVERT: J 51 GLU cc_start: 0.7995 (tt0) cc_final: 0.7676 (mm-30) REVERT: K 14 THR cc_start: 0.8211 (m) cc_final: 0.7801 (p) REVERT: K 41 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.7207 (mp10) REVERT: A 24 MET cc_start: 0.8969 (ptp) cc_final: 0.8707 (ptt) REVERT: B 8 ASP cc_start: 0.8372 (t70) cc_final: 0.8065 (t0) REVERT: B 68 LYS cc_start: 0.8900 (ptpp) cc_final: 0.8681 (ptpp) REVERT: B 101 ASP cc_start: 0.8012 (t0) cc_final: 0.7703 (t0) REVERT: B 118 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8592 (tt) REVERT: B 127 ASP cc_start: 0.8294 (m-30) cc_final: 0.8046 (m-30) REVERT: B 148 ASP cc_start: 0.8540 (m-30) cc_final: 0.8058 (m-30) REVERT: B 170 ARG cc_start: 0.8620 (mmt90) cc_final: 0.8312 (mmt90) REVERT: C 158 ASN cc_start: 0.8760 (p0) cc_final: 0.8547 (p0) REVERT: D 41 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8161 (tm-30) REVERT: E 51 GLU cc_start: 0.8529 (tp30) cc_final: 0.8122 (tp30) REVERT: G 42 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7509 (mtm180) REVERT: I 1 MET cc_start: 0.7496 (tpt) cc_final: 0.7159 (tpt) REVERT: I 41 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7477 (pm20) REVERT: L 24 GLU cc_start: 0.8058 (mp0) cc_final: 0.7818 (mp0) REVERT: L 60 ASN cc_start: 0.8358 (t0) cc_final: 0.7954 (t0) REVERT: L 62 GLN cc_start: 0.8449 (mp10) cc_final: 0.8156 (mp10) REVERT: L 64 GLU cc_start: 0.8343 (tm-30) cc_final: 0.7552 (tm-30) REVERT: M 14 ARG cc_start: 0.8292 (mtm110) cc_final: 0.7952 (ttp80) REVERT: M 63 GLN cc_start: 0.8833 (pp30) cc_final: 0.8310 (pp30) REVERT: N 11 TYR cc_start: 0.8918 (t80) cc_final: 0.8636 (t80) REVERT: O 93 GLN cc_start: 0.8999 (pp30) cc_final: 0.8751 (pp30) REVERT: O 95 TYR cc_start: 0.7748 (t80) cc_final: 0.7022 (t80) REVERT: P 49 SER cc_start: 0.9376 (m) cc_final: 0.8793 (p) REVERT: P 95 TYR cc_start: 0.6359 (t80) cc_final: 0.5967 (t80) outliers start: 35 outliers final: 21 residues processed: 381 average time/residue: 0.3315 time to fit residues: 182.8605 Evaluate side-chains 368 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 342 time to evaluate : 2.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 67 LEU 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 24 MET Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 118 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 4 PHE Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 52 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 90 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 40 GLN K 2 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.089299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.069214 restraints weight = 30471.658| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.74 r_work: 0.2893 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3141 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= 0.206 Angle : 0.657 12.471 19395 Z= 0.338 Chirality : 0.045 0.187 2255 Planarity : 0.004 0.045 2497 Dihedral : 4.662 53.365 1914 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.38 % Allowed : 22.89 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.21), residues: 1729 helix: 0.37 (0.16), residues: 1036 sheet: -1.31 (0.36), residues: 198 loop : 0.67 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 177 HIS 0.007 0.001 HIS A 111 PHE 0.015 0.001 PHE C 107 TYR 0.021 0.001 TYR N 95 ARG 0.008 0.001 ARG G 72 Details of bonding type rmsd hydrogen bonds : bond 0.03361 ( 728) hydrogen bonds : angle 4.74650 ( 2061) covalent geometry : bond 0.00491 (14312) covalent geometry : angle 0.65738 (19395) *********************** 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 381 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 344 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.7924 (tm-30) REVERT: H 21 ASP cc_start: 0.8510 (m-30) cc_final: 0.7951 (m-30) REVERT: H 41 GLN cc_start: 0.8846 (mp10) cc_final: 0.8022 (mp10) REVERT: F 21 ASP cc_start: 0.8541 (t0) cc_final: 0.8085 (t70) REVERT: F 50 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8118 (mp) REVERT: F 54 ARG cc_start: 0.7378 (mmt-90) cc_final: 0.6860 (mmt-90) REVERT: F 63 LYS cc_start: 0.8978 (ptpt) cc_final: 0.8704 (pttp) REVERT: J 18 GLU cc_start: 0.8856 (mp0) cc_final: 0.8439 (mp0) REVERT: J 21 ASP cc_start: 0.8169 (m-30) cc_final: 0.7128 (m-30) REVERT: J 31 GLN cc_start: 0.9042 (tp40) cc_final: 0.8823 (tp40) REVERT: K 14 THR cc_start: 0.8251 (m) cc_final: 0.7853 (p) REVERT: K 41 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.7202 (mp10) REVERT: A 24 MET cc_start: 0.9082 (ptp) cc_final: 0.8785 (ptt) REVERT: B 8 ASP cc_start: 0.8333 (t70) cc_final: 0.8033 (t0) REVERT: B 68 LYS cc_start: 0.8961 (ptpp) cc_final: 0.8731 (ptpp) REVERT: B 101 ASP cc_start: 0.8183 (t0) cc_final: 0.7781 (t0) REVERT: B 118 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8624 (tt) REVERT: B 127 ASP cc_start: 0.8416 (m-30) cc_final: 0.8154 (m-30) REVERT: B 148 ASP cc_start: 0.8608 (m-30) cc_final: 0.8142 (m-30) REVERT: B 170 ARG cc_start: 0.8677 (mmt90) cc_final: 0.8340 (mmt90) REVERT: C 147 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7942 (tp30) REVERT: D 41 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8220 (tm-30) REVERT: E 33 LYS cc_start: 0.8209 (mttt) cc_final: 0.7533 (pttm) REVERT: E 51 GLU cc_start: 0.8589 (tp30) cc_final: 0.8242 (tp30) REVERT: G 42 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7454 (mtm180) REVERT: I 1 MET cc_start: 0.7737 (tpt) cc_final: 0.7440 (tpt) REVERT: I 41 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7323 (pm20) REVERT: L 24 GLU cc_start: 0.8128 (mp0) cc_final: 0.7866 (mp0) REVERT: L 60 ASN cc_start: 0.8416 (t0) cc_final: 0.7987 (t0) REVERT: L 62 GLN cc_start: 0.8500 (mp10) cc_final: 0.8144 (mp10) REVERT: L 64 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7576 (tm-30) REVERT: M 14 ARG cc_start: 0.8355 (mtm110) cc_final: 0.7999 (ttp80) REVERT: M 63 GLN cc_start: 0.8918 (pp30) cc_final: 0.8395 (pp30) REVERT: M 93 GLN cc_start: 0.8561 (pp30) cc_final: 0.8332 (pp30) REVERT: O 40 ASP cc_start: 0.8684 (m-30) cc_final: 0.8459 (m-30) REVERT: P 1 MET cc_start: 0.7460 (mmt) cc_final: 0.7224 (mmm) REVERT: P 49 SER cc_start: 0.9359 (m) cc_final: 0.8709 (p) REVERT: P 95 TYR cc_start: 0.6546 (t80) cc_final: 0.6048 (t80) outliers start: 37 outliers final: 22 residues processed: 372 average time/residue: 0.2909 time to fit residues: 154.7538 Evaluate side-chains 371 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 341 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain F residue 50 LEU 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 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 B residue 118 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 147 GLU 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 E residue 12 THR Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 17 VAL 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 I residue 52 ASP Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 64 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 56 optimal weight: 0.4980 chunk 107 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 127 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 152 optimal weight: 0.0670 chunk 124 optimal weight: 7.9990 chunk 161 optimal weight: 10.0000 chunk 62 optimal weight: 0.2980 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 40 GLN K 2 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 = 0.3421 r_free = 0.3421 target = 0.090958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.070983 restraints weight = 30527.893| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.71 r_work: 0.2932 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14312 Z= 0.140 Angle : 0.645 11.786 19395 Z= 0.331 Chirality : 0.043 0.184 2255 Planarity : 0.004 0.043 2497 Dihedral : 4.629 54.038 1914 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.86 % Allowed : 23.92 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.21), residues: 1729 helix: 0.42 (0.17), residues: 1046 sheet: -1.23 (0.37), residues: 198 loop : 0.60 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 56 HIS 0.007 0.001 HIS A 111 PHE 0.013 0.001 PHE A 107 TYR 0.022 0.001 TYR N 95 ARG 0.008 0.000 ARG H 54 Details of bonding type rmsd hydrogen bonds : bond 0.03134 ( 728) hydrogen bonds : angle 4.68187 ( 2061) covalent geometry : bond 0.00333 (14312) covalent geometry : angle 0.64515 (19395) ********************** 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 387 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 358 time to evaluate : 1.748 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: 0.8708 (OUTLIER) cc_final: 0.7957 (tm-30) REVERT: H 21 ASP cc_start: 0.8494 (m-30) cc_final: 0.7981 (m-30) REVERT: H 41 GLN cc_start: 0.8862 (mp10) cc_final: 0.8052 (mp10) REVERT: F 21 ASP cc_start: 0.8386 (t0) cc_final: 0.7871 (t70) REVERT: F 54 ARG cc_start: 0.7382 (mmt-90) cc_final: 0.6822 (mmt-90) REVERT: F 63 LYS cc_start: 0.8942 (ptpt) cc_final: 0.8535 (ptmt) REVERT: J 18 GLU cc_start: 0.8837 (mp0) cc_final: 0.8433 (mp0) REVERT: J 21 ASP cc_start: 0.8152 (m-30) cc_final: 0.7086 (m-30) REVERT: J 31 GLN cc_start: 0.9026 (tp40) cc_final: 0.8388 (tp40) REVERT: J 51 GLU cc_start: 0.7993 (tt0) cc_final: 0.7678 (mm-30) REVERT: K 14 THR cc_start: 0.8209 (m) cc_final: 0.7848 (p) REVERT: K 41 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.7207 (mp10) REVERT: A 24 MET cc_start: 0.8994 (ptp) cc_final: 0.8778 (ptt) REVERT: B 8 ASP cc_start: 0.8413 (t70) cc_final: 0.8114 (t0) REVERT: B 68 LYS cc_start: 0.8902 (ptpp) cc_final: 0.8673 (ptpp) REVERT: B 101 ASP cc_start: 0.8076 (t0) cc_final: 0.7735 (t0) REVERT: B 118 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8601 (tt) REVERT: B 127 ASP cc_start: 0.8324 (m-30) cc_final: 0.8087 (m-30) REVERT: B 148 ASP cc_start: 0.8497 (m-30) cc_final: 0.8031 (m-30) REVERT: B 170 ARG cc_start: 0.8609 (mmt90) cc_final: 0.8314 (mmt90) REVERT: C 147 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7820 (tp30) REVERT: D 41 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8157 (tm-30) REVERT: E 51 GLU cc_start: 0.8550 (tp30) cc_final: 0.8158 (tp30) REVERT: G 2 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8209 (pp30) REVERT: G 42 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7492 (mtm180) REVERT: I 1 MET cc_start: 0.7546 (tpt) cc_final: 0.7216 (tpt) REVERT: I 41 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7488 (pm20) REVERT: L 11 LYS cc_start: 0.8771 (mtmm) cc_final: 0.8534 (mtmm) REVERT: L 24 GLU cc_start: 0.8115 (mp0) cc_final: 0.7850 (mp0) REVERT: L 60 ASN cc_start: 0.8381 (t0) cc_final: 0.7963 (t0) REVERT: L 62 GLN cc_start: 0.8462 (mp10) cc_final: 0.8162 (mp10) REVERT: M 14 ARG cc_start: 0.8310 (mtm110) cc_final: 0.7963 (ttp80) REVERT: M 63 GLN cc_start: 0.8857 (pp30) cc_final: 0.8340 (pp30) REVERT: N 11 TYR cc_start: 0.8891 (t80) cc_final: 0.8637 (t80) REVERT: O 40 ASP cc_start: 0.8623 (m-30) cc_final: 0.8385 (m-30) REVERT: P 1 MET cc_start: 0.7478 (mmt) cc_final: 0.7188 (mmm) REVERT: P 49 SER cc_start: 0.9354 (m) cc_final: 0.8726 (p) REVERT: P 95 TYR cc_start: 0.6481 (t80) cc_final: 0.5993 (t80) outliers start: 29 outliers final: 18 residues processed: 381 average time/residue: 0.3107 time to fit residues: 169.9001 Evaluate side-chains 367 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 343 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 73 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 B residue 118 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 158 ASN 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 12 THR Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain N residue 82 VAL 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 116 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 22 optimal weight: 30.0000 chunk 159 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 40 GLN K 2 GLN ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.094856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.075194 restraints weight = 30191.411| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.65 r_work: 0.2927 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3315 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= 0.189 Angle : 0.839 59.199 19395 Z= 0.475 Chirality : 0.047 0.931 2255 Planarity : 0.004 0.085 2497 Dihedral : 4.660 54.062 1914 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.80 % Allowed : 23.99 % Favored : 74.21 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.21), residues: 1729 helix: 0.43 (0.17), residues: 1046 sheet: -1.22 (0.37), residues: 198 loop : 0.60 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 56 HIS 0.006 0.001 HIS A 111 PHE 0.054 0.001 PHE L 4 TYR 0.017 0.001 TYR N 95 ARG 0.010 0.000 ARG O 65 Details of bonding type rmsd hydrogen bonds : bond 0.03145 ( 728) hydrogen bonds : angle 4.68353 ( 2061) covalent geometry : bond 0.00423 (14312) covalent geometry : angle 0.83859 (19395) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7379.87 seconds wall clock time: 134 minutes 19.04 seconds (8059.04 seconds total)