Starting phenix.real_space_refine on Tue Aug 26 06:20:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eat_27985/08_2025/8eat_27985.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eat_27985/08_2025/8eat_27985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eat_27985/08_2025/8eat_27985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eat_27985/08_2025/8eat_27985.map" model { file = "/net/cci-nas-00/data/ceres_data/8eat_27985/08_2025/8eat_27985.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eat_27985/08_2025/8eat_27985.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.194 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: 5 Type Number sf(0) Gaussians S 96 5.16 5 C 11238 2.51 5 N 2769 2.21 5 O 3097 1.98 5 H 17463 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34663 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1914 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 1253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1253 Classifications: {'peptide': 98} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain breaks: 1 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 95 Chain: "F" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1598 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 2, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "b" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 730 Classifications: {'peptide': 46} Link IDs: {'TRANS': 45} Chain: "c" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3008 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 195} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "d" Number of atoms: 5233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5233 Classifications: {'peptide': 338} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 1, 'TRP:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 41 Chain: "g" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 2334 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "h" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 2334 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "i" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 2334 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "j" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 2334 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "k" Number of atoms: 2329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 2329 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "l" Number of atoms: 2302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 2302 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "m" Number of atoms: 2339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2339 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "n" Number of atoms: 2313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2313 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "o" Number of atoms: 2308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 2308 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 151} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 5.27, per 1000 atoms: 0.15 Number of scatterers: 34663 At special positions: 0 Unit cell: (155.53, 107.12, 95.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 O 3097 8.00 N 2769 7.00 C 11238 6.00 H 17463 1.00 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: 3.21 Conformation dependent library (CDL) restraints added in 776.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4190 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 3 sheets defined 79.9% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 15 through 50 removed outlier: 3.938A pdb=" N ARG A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLY A 37 " --> pdb=" O GLN A 33 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASP A 40 " --> pdb=" O LYS A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 55 removed outlier: 4.192A pdb=" N ASP A 54 " --> pdb=" O TYR A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 137 Processing helix chain 'A' and resid 143 through 177 removed outlier: 3.717A pdb=" N ARG A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN A 148 " --> pdb=" O SER A 144 " (cutoff:3.500A) Proline residue: A 158 - end of helix Processing helix chain 'B' and resid 7 through 19 removed outlier: 3.609A pdb=" N ASN B 19 " --> pdb=" O ARG B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 38 Processing helix chain 'B' and resid 41 through 53 Processing helix chain 'B' and resid 84 through 105 removed outlier: 3.667A pdb=" N GLU B 102 " --> pdb=" O GLU B 98 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR B 103 " --> pdb=" O GLN B 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 24 Processing helix chain 'F' and resid 46 through 60 Processing helix chain 'F' and resid 71 through 77 Processing helix chain 'F' and resid 77 through 84 Processing helix chain 'F' and resid 102 through 105 Processing helix chain 'F' and resid 106 through 114 removed outlier: 3.629A pdb=" N LYS F 110 " --> pdb=" O ASP F 106 " (cutoff:3.500A) Processing helix chain 'b' and resid 220 through 246 Processing helix chain 'c' and resid 17 through 39 Processing helix chain 'c' and resid 41 through 45 Processing helix chain 'c' and resid 46 through 54 Processing helix chain 'c' and resid 55 through 91 removed outlier: 3.662A pdb=" N TRP c 59 " --> pdb=" O SER c 55 " (cutoff:3.500A) Processing helix chain 'c' and resid 95 through 123 removed outlier: 4.410A pdb=" N LYS c 99 " --> pdb=" O ARG c 95 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE c 102 " --> pdb=" O THR c 98 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER c 103 " --> pdb=" O LYS c 99 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE c 104 " --> pdb=" O ASN c 100 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL c 110 " --> pdb=" O PHE c 106 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA c 111 " --> pdb=" O CYS c 107 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL c 120 " --> pdb=" O ILE c 116 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER c 123 " --> pdb=" O ILE c 119 " (cutoff:3.500A) Processing helix chain 'c' and resid 135 through 177 Processing helix chain 'c' and resid 177 through 206 removed outlier: 3.998A pdb=" N PHE c 181 " --> pdb=" O ASP c 177 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL c 182 " --> pdb=" O SER c 178 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LYS c 183 " --> pdb=" O ALA c 179 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE c 187 " --> pdb=" O LYS c 183 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU c 194 " --> pdb=" O PHE c 190 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY c 195 " --> pdb=" O GLY c 191 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 7 removed outlier: 4.339A pdb=" N ASN d 7 " --> pdb=" O GLY d 3 " (cutoff:3.500A) Processing helix chain 'd' and resid 10 through 23 Processing helix chain 'd' and resid 26 through 36 Processing helix chain 'd' and resid 38 through 47 Processing helix chain 'd' and resid 64 through 86 Processing helix chain 'd' and resid 89 through 116 removed outlier: 3.715A pdb=" N GLY d 101 " --> pdb=" O TYR d 97 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR d 102 " --> pdb=" O ILE d 98 " (cutoff:3.500A) Processing helix chain 'd' and resid 119 through 124 Processing helix chain 'd' and resid 135 through 140 removed outlier: 4.367A pdb=" N SER d 140 " --> pdb=" O LEU d 136 " (cutoff:3.500A) Processing helix chain 'd' and resid 152 through 156 Processing helix chain 'd' and resid 158 through 163 removed outlier: 3.729A pdb=" N LYS d 163 " --> pdb=" O PRO d 160 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 200 Processing helix chain 'd' and resid 201 through 227 Processing helix chain 'd' and resid 234 through 242 Processing helix chain 'd' and resid 250 through 259 Processing helix chain 'd' and resid 261 through 271 Processing helix chain 'd' and resid 283 through 300 Processing helix chain 'd' and resid 306 through 333 removed outlier: 4.084A pdb=" N TRP d 310 " --> pdb=" O ILE d 306 " (cutoff:3.500A) Processing helix chain 'd' and resid 334 through 338 Processing helix chain 'g' and resid 8 through 44 removed outlier: 4.262A pdb=" N PHE g 12 " --> pdb=" O TYR g 8 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY g 13 " --> pdb=" O ALA g 9 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE g 21 " --> pdb=" O CYS g 17 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR g 24 " --> pdb=" O ALA g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 54 through 74 Processing helix chain 'g' and resid 83 through 122 removed outlier: 3.887A pdb=" N ARG g 117 " --> pdb=" O ASP g 113 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER g 120 " --> pdb=" O VAL g 116 " (cutoff:3.500A) Processing helix chain 'g' and resid 124 through 154 removed outlier: 4.262A pdb=" N GLY g 128 " --> pdb=" O ARG g 124 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU g 139 " --> pdb=" O PHE g 135 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY g 140 " --> pdb=" O ALA g 136 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU g 141 " --> pdb=" O GLU g 137 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL g 146 " --> pdb=" O TYR g 142 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA g 154 " --> pdb=" O LEU g 150 " (cutoff:3.500A) Processing helix chain 'h' and resid 8 through 43 removed outlier: 4.079A pdb=" N PHE h 12 " --> pdb=" O TYR h 8 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY h 13 " --> pdb=" O ALA h 9 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE h 21 " --> pdb=" O CYS h 17 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR h 24 " --> pdb=" O ALA h 20 " (cutoff:3.500A) Processing helix chain 'h' and resid 46 through 48 No H-bonds generated for 'chain 'h' and resid 46 through 48' Processing helix chain 'h' and resid 49 through 54 Processing helix chain 'h' and resid 54 through 76 Processing helix chain 'h' and resid 83 through 122 removed outlier: 3.951A pdb=" N SER h 120 " --> pdb=" O VAL h 116 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLN h 121 " --> pdb=" O ARG h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 124 through 154 removed outlier: 4.259A pdb=" N GLY h 128 " --> pdb=" O ARG h 124 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU h 139 " --> pdb=" O PHE h 135 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY h 140 " --> pdb=" O ALA h 136 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY h 143 " --> pdb=" O LEU h 139 " (cutoff:3.500A) Processing helix chain 'i' and resid 8 through 43 removed outlier: 4.071A pdb=" N PHE i 12 " --> pdb=" O TYR i 8 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY i 13 " --> pdb=" O ALA i 9 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE i 21 " --> pdb=" O CYS i 17 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR i 24 " --> pdb=" O ALA i 20 " (cutoff:3.500A) Processing helix chain 'i' and resid 46 through 48 No H-bonds generated for 'chain 'i' and resid 46 through 48' Processing helix chain 'i' and resid 49 through 54 Processing helix chain 'i' and resid 54 through 76 Processing helix chain 'i' and resid 83 through 122 removed outlier: 3.854A pdb=" N SER i 120 " --> pdb=" O VAL i 116 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLN i 121 " --> pdb=" O ARG i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 125 through 155 removed outlier: 3.894A pdb=" N LEU i 139 " --> pdb=" O PHE i 135 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY i 140 " --> pdb=" O ALA i 136 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR i 155 " --> pdb=" O ASN i 151 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 44 removed outlier: 4.193A pdb=" N PHE j 12 " --> pdb=" O TYR j 8 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY j 13 " --> pdb=" O ALA j 9 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE j 21 " --> pdb=" O CYS j 17 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR j 24 " --> pdb=" O ALA j 20 " (cutoff:3.500A) Processing helix chain 'j' and resid 46 through 48 No H-bonds generated for 'chain 'j' and resid 46 through 48' Processing helix chain 'j' and resid 49 through 54 Processing helix chain 'j' and resid 54 through 77 Processing helix chain 'j' and resid 83 through 120 Processing helix chain 'j' and resid 124 through 153 removed outlier: 4.299A pdb=" N GLY j 128 " --> pdb=" O ARG j 124 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU j 139 " --> pdb=" O PHE j 135 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY j 140 " --> pdb=" O ALA j 136 " (cutoff:3.500A) Processing helix chain 'k' and resid 8 through 43 removed outlier: 4.248A pdb=" N PHE k 12 " --> pdb=" O TYR k 8 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY k 13 " --> pdb=" O ALA k 9 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE k 23 " --> pdb=" O SER k 19 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR k 24 " --> pdb=" O ALA k 20 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 50 Processing helix chain 'k' and resid 54 through 78 Processing helix chain 'k' and resid 83 through 122 removed outlier: 3.805A pdb=" N GLN k 121 " --> pdb=" O ARG k 117 " (cutoff:3.500A) Processing helix chain 'k' and resid 124 through 153 removed outlier: 4.234A pdb=" N GLY k 128 " --> pdb=" O ARG k 124 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU k 139 " --> pdb=" O PHE k 135 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY k 140 " --> pdb=" O ALA k 136 " (cutoff:3.500A) Processing helix chain 'l' and resid 8 through 43 removed outlier: 4.364A pdb=" N PHE l 12 " --> pdb=" O TYR l 8 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY l 13 " --> pdb=" O ALA l 9 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE l 21 " --> pdb=" O CYS l 17 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR l 24 " --> pdb=" O ALA l 20 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR l 30 " --> pdb=" O LEU l 26 " (cutoff:3.500A) Processing helix chain 'l' and resid 46 through 50 removed outlier: 3.551A pdb=" N LEU l 49 " --> pdb=" O ARG l 46 " (cutoff:3.500A) Processing helix chain 'l' and resid 54 through 77 Processing helix chain 'l' and resid 83 through 120 removed outlier: 3.615A pdb=" N SER l 120 " --> pdb=" O VAL l 116 " (cutoff:3.500A) Processing helix chain 'l' and resid 124 through 154 removed outlier: 4.115A pdb=" N GLY l 128 " --> pdb=" O ARG l 124 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY l 140 " --> pdb=" O ALA l 136 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU l 150 " --> pdb=" O VAL l 146 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA l 154 " --> pdb=" O LEU l 150 " (cutoff:3.500A) Processing helix chain 'm' and resid 8 through 43 removed outlier: 4.304A pdb=" N PHE m 12 " --> pdb=" O TYR m 8 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY m 13 " --> pdb=" O ALA m 9 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE m 21 " --> pdb=" O CYS m 17 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR m 24 " --> pdb=" O ALA m 20 " (cutoff:3.500A) Processing helix chain 'm' and resid 46 through 48 No H-bonds generated for 'chain 'm' and resid 46 through 48' Processing helix chain 'm' and resid 49 through 54 Processing helix chain 'm' and resid 54 through 76 removed outlier: 3.702A pdb=" N ILE m 63 " --> pdb=" O MET m 59 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA m 64 " --> pdb=" O ALA m 60 " (cutoff:3.500A) Processing helix chain 'm' and resid 83 through 120 removed outlier: 3.722A pdb=" N ALA m 103 " --> pdb=" O LEU m 99 " (cutoff:3.500A) Processing helix chain 'm' and resid 122 through 124 No H-bonds generated for 'chain 'm' and resid 122 through 124' Processing helix chain 'm' and resid 125 through 154 removed outlier: 3.913A pdb=" N LEU m 139 " --> pdb=" O PHE m 135 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY m 140 " --> pdb=" O ALA m 136 " (cutoff:3.500A) Processing helix chain 'n' and resid 8 through 44 removed outlier: 4.247A pdb=" N PHE n 12 " --> pdb=" O TYR n 8 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY n 13 " --> pdb=" O ALA n 9 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL n 44 " --> pdb=" O CYS n 40 " (cutoff:3.500A) Processing helix chain 'n' and resid 49 through 54 Processing helix chain 'n' and resid 54 through 78 Processing helix chain 'n' and resid 83 through 122 removed outlier: 3.872A pdb=" N ARG n 117 " --> pdb=" O ASP n 113 " (cutoff:3.500A) Processing helix chain 'n' and resid 125 through 154 removed outlier: 3.980A pdb=" N LEU n 139 " --> pdb=" O PHE n 135 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY n 140 " --> pdb=" O ALA n 136 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 48 removed outlier: 4.069A pdb=" N PHE o 18 " --> pdb=" O TYR o 14 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 51 No H-bonds generated for 'chain 'o' and resid 49 through 51' Processing helix chain 'o' and resid 60 through 83 Processing helix chain 'o' and resid 91 through 122 Processing helix chain 'o' and resid 130 through 132 No H-bonds generated for 'chain 'o' and resid 130 through 132' Processing helix chain 'o' and resid 133 through 164 removed outlier: 3.622A pdb=" N LEU o 139 " --> pdb=" O VAL o 135 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU o 147 " --> pdb=" O PHE o 143 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY o 148 " --> pdb=" O SER o 144 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY o 151 " --> pdb=" O LEU o 147 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR o 160 " --> pdb=" O LEU o 156 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 77 Processing sheet with id=AA2, first strand: chain 'B' and resid 39 through 40 Processing sheet with id=AA3, first strand: chain 'F' and resid 37 through 39 removed outlier: 6.441A pdb=" N LEU F 7 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE F 66 " --> pdb=" O LEU F 7 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA F 65 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU F 92 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU F 67 " --> pdb=" O LEU F 92 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE F 94 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE F 69 " --> pdb=" O ILE F 94 " (cutoff:3.500A) 1433 hydrogen bonds defined for protein. 4248 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: 8.54 Time building geometry restraints manager: 4.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17407 1.03 - 1.23: 126 1.23 - 1.42: 7036 1.42 - 1.62: 10258 1.62 - 1.81: 136 Bond restraints: 34963 Sorted by residual: bond pdb=" CB GLN n 82 " pdb=" CG GLN n 82 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.73e+00 bond pdb=" N GLY o 106 " pdb=" CA GLY o 106 " ideal model delta sigma weight residual 1.454 1.440 0.014 1.24e-02 6.50e+03 1.35e+00 bond pdb=" CB VAL o 105 " pdb=" CG2 VAL o 105 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.28e+00 bond pdb=" N PRO B 68 " pdb=" CA PRO B 68 " ideal model delta sigma weight residual 1.469 1.483 -0.014 1.28e-02 6.10e+03 1.20e+00 bond pdb=" N GLY o 117 " pdb=" CA GLY o 117 " ideal model delta sigma weight residual 1.454 1.441 0.013 1.24e-02 6.50e+03 1.11e+00 ... (remaining 34958 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 60345 1.18 - 2.36: 2772 2.36 - 3.54: 128 3.54 - 4.72: 43 4.72 - 5.90: 5 Bond angle restraints: 63293 Sorted by residual: angle pdb=" C ILE j 54 " pdb=" N VAL j 55 " pdb=" CA VAL j 55 " ideal model delta sigma weight residual 120.33 122.66 -2.33 8.00e-01 1.56e+00 8.48e+00 angle pdb=" N VAL l 146 " pdb=" CA VAL l 146 " pdb=" C VAL l 146 " ideal model delta sigma weight residual 111.91 109.40 2.51 8.90e-01 1.26e+00 7.97e+00 angle pdb=" N VAL m 55 " pdb=" CA VAL m 55 " pdb=" CB VAL m 55 " ideal model delta sigma weight residual 110.50 112.23 -1.73 6.30e-01 2.52e+00 7.52e+00 angle pdb=" C VAL m 55 " pdb=" CA VAL m 55 " pdb=" CB VAL m 55 " ideal model delta sigma weight residual 114.35 111.50 2.85 1.06e+00 8.90e-01 7.25e+00 angle pdb=" C VAL i 55 " pdb=" CA VAL i 55 " pdb=" CB VAL i 55 " ideal model delta sigma weight residual 114.00 110.62 3.38 1.31e+00 5.83e-01 6.65e+00 ... (remaining 63288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 14844 17.96 - 35.92: 933 35.92 - 53.87: 414 53.87 - 71.83: 222 71.83 - 89.79: 27 Dihedral angle restraints: 16440 sinusoidal: 8733 harmonic: 7707 Sorted by residual: dihedral pdb=" CA ASN A 49 " pdb=" C ASN A 49 " pdb=" N TYR A 50 " pdb=" CA TYR A 50 " ideal model delta harmonic sigma weight residual 180.00 157.21 22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA GLY o 123 " pdb=" C GLY o 123 " pdb=" N VAL o 124 " pdb=" CA VAL o 124 " ideal model delta harmonic sigma weight residual 180.00 161.06 18.94 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA VAL F 10 " pdb=" C VAL F 10 " pdb=" N ILE F 11 " pdb=" CA ILE F 11 " ideal model delta harmonic sigma weight residual 180.00 161.48 18.52 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 16437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1715 0.026 - 0.051: 728 0.051 - 0.077: 313 0.077 - 0.103: 111 0.103 - 0.129: 33 Chirality restraints: 2900 Sorted by residual: chirality pdb=" CA ILE F 28 " pdb=" N ILE F 28 " pdb=" C ILE F 28 " pdb=" CB ILE F 28 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA ILE F 69 " pdb=" N ILE F 69 " pdb=" C ILE F 69 " pdb=" CB ILE F 69 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA ILE d 200 " pdb=" N ILE d 200 " pdb=" C ILE d 200 " pdb=" CB ILE d 200 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 2897 not shown) Planarity restraints: 5232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS o 52 " 0.068 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO o 53 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO o 53 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO o 53 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE d 192 " -0.019 2.00e-02 2.50e+03 1.29e-02 4.96e+00 pdb=" CG PHE d 192 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE d 192 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE d 192 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE d 192 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE d 192 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE d 192 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE d 192 " 0.003 2.00e-02 2.50e+03 pdb=" HD2 PHE d 192 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE d 192 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE d 192 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE d 192 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP c 77 " -0.013 2.00e-02 2.50e+03 1.10e-02 4.85e+00 pdb=" CG TRP c 77 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP c 77 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP c 77 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP c 77 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP c 77 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP c 77 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP c 77 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP c 77 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP c 77 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 TRP c 77 " -0.008 2.00e-02 2.50e+03 pdb=" HE1 TRP c 77 " -0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP c 77 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP c 77 " 0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP c 77 " -0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP c 77 " -0.000 2.00e-02 2.50e+03 ... (remaining 5229 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 517 2.08 - 2.71: 60505 2.71 - 3.34: 112190 3.34 - 3.97: 139754 3.97 - 4.60: 226135 Nonbonded interactions: 539101 Sorted by model distance: nonbonded pdb="HE22 GLN n 82 " pdb=" OE1 GLN n 90 " model vdw 1.454 2.450 nonbonded pdb=" O ASN c 132 " pdb="HD21 ASN c 138 " model vdw 1.526 2.450 nonbonded pdb=" OD2 ASP d 217 " pdb=" HH TYR d 275 " model vdw 1.639 2.450 nonbonded pdb="HD22 ASN c 138 " pdb=" OXT GLN c 213 " model vdw 1.663 2.450 nonbonded pdb=" O ASP d 298 " pdb=" HG1 THR d 301 " model vdw 1.672 2.450 ... (remaining 539096 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 'g' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name HA )) or resid 3 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 44 or (resid 45 through 4 \ 6 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 47 or (resid 48 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 49 through 121 or (resid 122 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 123 or (resi \ d 124 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 125 through 159)) selection = (chain 'h' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name HA )) or resid 3 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 44 or (resid 45 through 4 \ 6 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 47 or (resid 48 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 49 through 121 or (resid 122 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 123 or (resi \ d 124 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 125 through 159)) selection = (chain 'i' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name HA )) or resid 3 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 44 or (resid 45 through 4 \ 6 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 47 or (resid 48 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 49 through 121 or (resid 122 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 123 or (resi \ d 124 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 125 through 159)) selection = (chain 'j' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name HA )) or resid 3 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 44 or (resid 45 through 4 \ 6 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 47 or (resid 48 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 49 through 121 or (resid 122 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 123 or (resi \ d 124 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 125 through 159)) selection = (chain 'k' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name HA )) or resid 3 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 44 or (resid 45 through 4 \ 6 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 47 through 121 or (resid 122 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 123 or (resid 124 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 125 throug \ h 159)) selection = (chain 'l' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name HA )) or resid 3 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 44 or (resid 45 through 4 \ 6 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 47 through 159)) selection = (chain 'm' and (resid 2 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 44 or (resid 45 through 4 \ 6 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 47 or (resid 48 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 49 through 121 or (resid 122 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 123 or (resi \ d 124 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 125 through 159)) selection = (chain 'n' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name HA )) or resid 3 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 49 through 121 or (resid \ 122 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 123 or (resid 124 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 125 through 159)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.710 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: 0.210 Extract box with map and model: 0.380 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 30.220 Find NCS groups from input model: 0.370 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: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17500 Z= 0.201 Angle : 0.544 5.899 23787 Z= 0.329 Chirality : 0.037 0.129 2900 Planarity : 0.004 0.104 2969 Dihedral : 12.777 89.789 6002 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.17), residues: 2313 helix: 0.31 (0.12), residues: 1705 sheet: -0.66 (0.92), residues: 30 loop : -0.37 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG d 181 TYR 0.023 0.001 TYR d 185 PHE 0.038 0.001 PHE d 192 TRP 0.035 0.002 TRP c 77 HIS 0.003 0.001 HIS d 78 Details of bonding type rmsd covalent geometry : bond 0.00409 (17500) covalent geometry : angle 0.54353 (23787) hydrogen bonds : bond 0.16690 ( 1433) hydrogen bonds : angle 8.23520 ( 4248) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 17 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue TYR 52 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 233 is missing expected H atoms. Skipping. Residue THR 2 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Evaluate side-chains 226 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.2750 time to fit residues: 92.6485 Evaluate side-chains 197 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.6980 chunk 212 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN l 121 GLN n 122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.144828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.099717 restraints weight = 50508.100| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.51 r_work: 0.3124 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17500 Z= 0.199 Angle : 0.539 7.201 23787 Z= 0.299 Chirality : 0.038 0.131 2900 Planarity : 0.004 0.088 2969 Dihedral : 4.222 52.885 2496 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.51 % Allowed : 3.65 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.17), residues: 2313 helix: 1.46 (0.12), residues: 1740 sheet: -1.08 (0.87), residues: 30 loop : -0.23 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 80 TYR 0.013 0.001 TYR A 50 PHE 0.029 0.001 PHE c 80 TRP 0.014 0.001 TRP c 77 HIS 0.003 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00412 (17500) covalent geometry : angle 0.53912 (23787) hydrogen bonds : bond 0.06075 ( 1433) hydrogen bonds : angle 5.01375 ( 4248) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 17 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue TYR 52 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 233 is missing expected H atoms. Skipping. Residue THR 2 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 207 time to evaluate : 0.568 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: d 199 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7602 (mp0) REVERT: d 274 GLU cc_start: 0.6693 (tp30) cc_final: 0.6380 (tt0) REVERT: n 122 GLN cc_start: 0.8338 (tp-100) cc_final: 0.8122 (tp-100) REVERT: n 129 MET cc_start: 0.7128 (ttp) cc_final: 0.6706 (ttp) outliers start: 9 outliers final: 7 residues processed: 211 average time/residue: 0.2607 time to fit residues: 84.3605 Evaluate side-chains 206 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 199 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain b residue 247 LEU Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 150 ILE Chi-restraints excluded: chain h residue 129 MET Chi-restraints excluded: chain h residue 151 ASN Chi-restraints excluded: chain o residue 89 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 18 optimal weight: 0.4980 chunk 205 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 194 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN d 176 ASN l 121 GLN o 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.145081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.100182 restraints weight = 50294.102| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.51 r_work: 0.3131 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17500 Z= 0.180 Angle : 0.495 5.431 23787 Z= 0.275 Chirality : 0.037 0.131 2900 Planarity : 0.004 0.086 2969 Dihedral : 4.135 50.855 2496 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.63 % Allowed : 4.91 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.17), residues: 2313 helix: 1.68 (0.12), residues: 1736 sheet: -1.04 (0.89), residues: 30 loop : -0.18 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 80 TYR 0.010 0.001 TYR o 127 PHE 0.027 0.001 PHE c 80 TRP 0.012 0.001 TRP c 77 HIS 0.003 0.001 HIS d 128 Details of bonding type rmsd covalent geometry : bond 0.00370 (17500) covalent geometry : angle 0.49539 (23787) hydrogen bonds : bond 0.05553 ( 1433) hydrogen bonds : angle 4.70208 ( 4248) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 17 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue TYR 52 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 233 is missing expected H atoms. Skipping. Residue THR 2 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 197 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 199 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7546 (mp0) REVERT: g 59 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7894 (mtt) REVERT: j 35 SER cc_start: 0.8780 (t) cc_final: 0.8418 (m) REVERT: n 129 MET cc_start: 0.7073 (ttp) cc_final: 0.6758 (ttp) REVERT: o 54 GLU cc_start: 0.5858 (pm20) cc_final: 0.5596 (pm20) outliers start: 11 outliers final: 6 residues processed: 203 average time/residue: 0.2583 time to fit residues: 80.7142 Evaluate side-chains 198 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 191 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain c residue 150 ILE Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain h residue 129 MET Chi-restraints excluded: chain h residue 151 ASN Chi-restraints excluded: chain o residue 89 ASP Chi-restraints excluded: chain o residue 159 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 170 optimal weight: 1.9990 chunk 220 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 104 optimal weight: 0.0070 chunk 176 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.145896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.100605 restraints weight = 50336.587| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.57 r_work: 0.3146 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17500 Z= 0.150 Angle : 0.470 5.306 23787 Z= 0.260 Chirality : 0.036 0.128 2900 Planarity : 0.004 0.072 2969 Dihedral : 4.028 46.994 2496 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.40 % Allowed : 5.82 % Favored : 93.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.17), residues: 2313 helix: 1.82 (0.12), residues: 1740 sheet: -0.97 (0.90), residues: 30 loop : -0.04 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 80 TYR 0.011 0.001 TYR A 50 PHE 0.023 0.001 PHE c 80 TRP 0.008 0.001 TRP d 312 HIS 0.002 0.001 HIS d 128 Details of bonding type rmsd covalent geometry : bond 0.00295 (17500) covalent geometry : angle 0.47049 (23787) hydrogen bonds : bond 0.05158 ( 1433) hydrogen bonds : angle 4.48970 ( 4248) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 17 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue TYR 52 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 233 is missing expected H atoms. Skipping. Residue THR 2 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 202 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 199 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7610 (mp0) REVERT: g 59 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7699 (mtt) REVERT: j 35 SER cc_start: 0.8724 (t) cc_final: 0.8514 (m) REVERT: n 129 MET cc_start: 0.7043 (ttp) cc_final: 0.6754 (ttp) outliers start: 7 outliers final: 5 residues processed: 207 average time/residue: 0.2587 time to fit residues: 82.2993 Evaluate side-chains 198 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 192 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain c residue 150 ILE Chi-restraints excluded: chain d residue 251 LEU Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain h residue 151 ASN Chi-restraints excluded: chain o residue 89 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 30 optimal weight: 0.0770 chunk 7 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 213 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 137 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** n 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 83 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.145260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.100214 restraints weight = 50473.929| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.52 r_work: 0.3138 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17500 Z= 0.178 Angle : 0.481 5.526 23787 Z= 0.266 Chirality : 0.037 0.145 2900 Planarity : 0.004 0.066 2969 Dihedral : 4.001 44.805 2496 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.74 % Allowed : 6.22 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.17), residues: 2313 helix: 1.85 (0.12), residues: 1738 sheet: -1.01 (0.89), residues: 30 loop : -0.07 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 80 TYR 0.010 0.001 TYR A 50 PHE 0.026 0.001 PHE c 80 TRP 0.008 0.001 TRP c 77 HIS 0.003 0.001 HIS F 56 Details of bonding type rmsd covalent geometry : bond 0.00370 (17500) covalent geometry : angle 0.48081 (23787) hydrogen bonds : bond 0.05150 ( 1433) hydrogen bonds : angle 4.45527 ( 4248) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 17 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue TYR 52 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 233 is missing expected H atoms. Skipping. Residue THR 2 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 193 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7964 (tpt) cc_final: 0.7725 (tpp) REVERT: F 48 GLU cc_start: 0.7055 (mp0) cc_final: 0.6801 (tm-30) REVERT: c 80 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.8737 (p90) REVERT: d 179 ILE cc_start: 0.7801 (mm) cc_final: 0.7433 (mm) REVERT: d 199 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7604 (mp0) REVERT: d 223 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7404 (mp) REVERT: g 59 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7654 (mtt) REVERT: l 50 LEU cc_start: 0.8347 (tp) cc_final: 0.8099 (tt) REVERT: n 129 MET cc_start: 0.7051 (ttp) cc_final: 0.6744 (ttp) outliers start: 13 outliers final: 8 residues processed: 200 average time/residue: 0.2682 time to fit residues: 81.2066 Evaluate side-chains 201 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 190 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain b residue 247 LEU Chi-restraints excluded: chain c residue 80 PHE Chi-restraints excluded: chain c residue 150 ILE Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain d residue 251 LEU Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain h residue 129 MET Chi-restraints excluded: chain h residue 151 ASN Chi-restraints excluded: chain o residue 89 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 212 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 217 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** n 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 159 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 = 0.3805 r_free = 0.3805 target = 0.143864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.098397 restraints weight = 50696.212| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.57 r_work: 0.3146 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17500 Z= 0.153 Angle : 0.466 5.347 23787 Z= 0.257 Chirality : 0.036 0.141 2900 Planarity : 0.004 0.061 2969 Dihedral : 3.933 41.830 2496 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.74 % Allowed : 7.13 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.17), residues: 2313 helix: 1.98 (0.12), residues: 1738 sheet: -1.03 (0.88), residues: 30 loop : -0.05 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 57 TYR 0.010 0.001 TYR A 51 PHE 0.021 0.001 PHE c 80 TRP 0.007 0.001 TRP c 77 HIS 0.002 0.001 HIS F 72 Details of bonding type rmsd covalent geometry : bond 0.00309 (17500) covalent geometry : angle 0.46638 (23787) hydrogen bonds : bond 0.04969 ( 1433) hydrogen bonds : angle 4.34722 ( 4248) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 17 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue TYR 52 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 233 is missing expected H atoms. Skipping. Residue THR 2 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 196 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLN cc_start: 0.4078 (mm110) cc_final: 0.3829 (mm-40) REVERT: B 1 MET cc_start: 0.7933 (tpt) cc_final: 0.7205 (tpp) REVERT: F 48 GLU cc_start: 0.7354 (mp0) cc_final: 0.7129 (tm-30) REVERT: c 80 PHE cc_start: 0.9017 (OUTLIER) cc_final: 0.8739 (p90) REVERT: d 179 ILE cc_start: 0.7825 (mm) cc_final: 0.7463 (mm) REVERT: d 223 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.7423 (mp) REVERT: g 59 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7528 (mtt) REVERT: l 50 LEU cc_start: 0.8315 (tp) cc_final: 0.8095 (tt) REVERT: n 129 MET cc_start: 0.7091 (ttp) cc_final: 0.6797 (ttp) REVERT: n 159 VAL cc_start: 0.8914 (p) cc_final: 0.8621 (m) outliers start: 13 outliers final: 6 residues processed: 202 average time/residue: 0.2760 time to fit residues: 84.3526 Evaluate side-chains 201 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 192 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain c residue 80 PHE Chi-restraints excluded: chain c residue 150 ILE Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain d residue 251 LEU Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain h residue 129 MET Chi-restraints excluded: chain h residue 151 ASN Chi-restraints excluded: chain o residue 89 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** n 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 83 ASN o 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.143587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.098470 restraints weight = 50739.253| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.52 r_work: 0.3094 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 17500 Z= 0.286 Angle : 0.539 6.652 23787 Z= 0.300 Chirality : 0.039 0.150 2900 Planarity : 0.004 0.061 2969 Dihedral : 4.118 45.058 2496 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.74 % Allowed : 7.87 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.17), residues: 2313 helix: 1.65 (0.12), residues: 1738 sheet: -1.12 (0.91), residues: 29 loop : -0.26 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 57 TYR 0.010 0.002 TYR d 51 PHE 0.029 0.002 PHE c 80 TRP 0.010 0.001 TRP c 77 HIS 0.007 0.001 HIS F 56 Details of bonding type rmsd covalent geometry : bond 0.00639 (17500) covalent geometry : angle 0.53925 (23787) hydrogen bonds : bond 0.05428 ( 1433) hydrogen bonds : angle 4.58386 ( 4248) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 17 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue TYR 52 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 233 is missing expected H atoms. Skipping. Residue THR 2 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 194 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 48 GLU cc_start: 0.7329 (mp0) cc_final: 0.7093 (tm-30) REVERT: F 49 GLU cc_start: 0.7399 (mp0) cc_final: 0.7133 (pm20) REVERT: c 80 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.8902 (p90) REVERT: d 179 ILE cc_start: 0.7859 (mm) cc_final: 0.7494 (mm) REVERT: g 59 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7742 (mtt) REVERT: l 50 LEU cc_start: 0.8310 (tp) cc_final: 0.8094 (tt) REVERT: n 129 MET cc_start: 0.7143 (ttp) cc_final: 0.6838 (ttp) REVERT: n 159 VAL cc_start: 0.8927 (p) cc_final: 0.8638 (m) outliers start: 13 outliers final: 9 residues processed: 200 average time/residue: 0.2648 time to fit residues: 80.4268 Evaluate side-chains 196 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 185 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain b residue 247 LEU Chi-restraints excluded: chain c residue 80 PHE Chi-restraints excluded: chain c residue 150 ILE Chi-restraints excluded: chain d residue 251 LEU Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain h residue 129 MET Chi-restraints excluded: chain h residue 151 ASN Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain o residue 89 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 55 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 209 optimal weight: 0.4980 chunk 220 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** n 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 83 ASN o 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.143281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.097749 restraints weight = 50508.329| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.58 r_work: 0.3122 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17500 Z= 0.145 Angle : 0.477 6.773 23787 Z= 0.261 Chirality : 0.036 0.170 2900 Planarity : 0.004 0.059 2969 Dihedral : 3.979 42.508 2496 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.51 % Allowed : 8.39 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.09 (0.17), residues: 2313 helix: 1.91 (0.12), residues: 1740 sheet: -1.09 (0.90), residues: 29 loop : -0.11 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 57 TYR 0.012 0.001 TYR d 289 PHE 0.021 0.001 PHE c 80 TRP 0.007 0.001 TRP d 312 HIS 0.006 0.001 HIS F 56 Details of bonding type rmsd covalent geometry : bond 0.00288 (17500) covalent geometry : angle 0.47662 (23787) hydrogen bonds : bond 0.05015 ( 1433) hydrogen bonds : angle 4.37541 ( 4248) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 17 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue TYR 52 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 233 is missing expected H atoms. Skipping. Residue THR 2 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Evaluate side-chains 204 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 195 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8004 (tpt) cc_final: 0.7361 (tpp) REVERT: c 80 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.8813 (p90) REVERT: d 179 ILE cc_start: 0.7788 (mm) cc_final: 0.7429 (mm) REVERT: g 59 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7503 (mtt) REVERT: m 5 CYS cc_start: 0.8070 (p) cc_final: 0.7818 (p) REVERT: n 129 MET cc_start: 0.7070 (ttp) cc_final: 0.6769 (ttp) REVERT: n 159 VAL cc_start: 0.8910 (p) cc_final: 0.8614 (m) outliers start: 9 outliers final: 7 residues processed: 199 average time/residue: 0.2696 time to fit residues: 82.3173 Evaluate side-chains 203 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 194 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain c residue 80 PHE Chi-restraints excluded: chain c residue 150 ILE Chi-restraints excluded: chain d residue 251 LEU Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain h residue 129 MET Chi-restraints excluded: chain h residue 151 ASN Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain o residue 89 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 124 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 221 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** n 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.144225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.099316 restraints weight = 50403.406| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.51 r_work: 0.3124 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17500 Z= 0.194 Angle : 0.496 7.072 23787 Z= 0.274 Chirality : 0.037 0.144 2900 Planarity : 0.004 0.057 2969 Dihedral : 3.997 41.667 2496 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.63 % Allowed : 8.27 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.17), residues: 2313 helix: 1.85 (0.12), residues: 1743 sheet: -1.18 (0.91), residues: 29 loop : -0.09 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 57 TYR 0.009 0.001 TYR c 57 PHE 0.025 0.001 PHE c 80 TRP 0.007 0.001 TRP d 312 HIS 0.007 0.001 HIS F 56 Details of bonding type rmsd covalent geometry : bond 0.00413 (17500) covalent geometry : angle 0.49635 (23787) hydrogen bonds : bond 0.05103 ( 1433) hydrogen bonds : angle 4.41497 ( 4248) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 17 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue TYR 52 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 233 is missing expected H atoms. Skipping. Residue THR 2 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 188 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7997 (tpt) cc_final: 0.7395 (tpp) REVERT: c 80 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8880 (p90) REVERT: d 179 ILE cc_start: 0.7814 (mm) cc_final: 0.7447 (mm) REVERT: g 59 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7574 (mtt) REVERT: m 5 CYS cc_start: 0.8071 (p) cc_final: 0.7818 (p) REVERT: n 129 MET cc_start: 0.7128 (ttp) cc_final: 0.6820 (ttp) REVERT: n 131 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8002 (mp) REVERT: n 159 VAL cc_start: 0.8918 (p) cc_final: 0.8625 (m) outliers start: 11 outliers final: 7 residues processed: 192 average time/residue: 0.2522 time to fit residues: 74.8040 Evaluate side-chains 196 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 186 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain c residue 80 PHE Chi-restraints excluded: chain c residue 150 ILE Chi-restraints excluded: chain d residue 251 LEU Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain h residue 129 MET Chi-restraints excluded: chain h residue 151 ASN Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain n residue 131 LEU Chi-restraints excluded: chain o residue 89 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 217 optimal weight: 0.9990 chunk 209 optimal weight: 0.1980 chunk 220 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 chunk 152 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 156 GLN ** n 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 83 ASN o 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.144546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.100333 restraints weight = 51324.923| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.49 r_work: 0.3174 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17500 Z= 0.170 Angle : 0.481 5.789 23787 Z= 0.265 Chirality : 0.037 0.138 2900 Planarity : 0.004 0.057 2969 Dihedral : 3.961 40.478 2496 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.63 % Allowed : 8.56 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.17), residues: 2313 helix: 1.94 (0.12), residues: 1743 sheet: -1.21 (0.91), residues: 29 loop : -0.04 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 57 TYR 0.009 0.001 TYR A 50 PHE 0.025 0.001 PHE B 93 TRP 0.007 0.001 TRP d 312 HIS 0.012 0.001 HIS F 56 Details of bonding type rmsd covalent geometry : bond 0.00353 (17500) covalent geometry : angle 0.48109 (23787) hydrogen bonds : bond 0.04982 ( 1433) hydrogen bonds : angle 4.35413 ( 4248) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 17 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue TYR 52 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 233 is missing expected H atoms. Skipping. Residue THR 2 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 185 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8076 (tpt) cc_final: 0.7536 (tpp) REVERT: c 80 PHE cc_start: 0.9132 (OUTLIER) cc_final: 0.8905 (p90) REVERT: d 179 ILE cc_start: 0.8000 (mm) cc_final: 0.7631 (mm) REVERT: j 3 GLU cc_start: 0.7997 (pt0) cc_final: 0.7590 (tt0) REVERT: m 5 CYS cc_start: 0.8183 (p) cc_final: 0.7927 (p) REVERT: n 129 MET cc_start: 0.7336 (ttp) cc_final: 0.7034 (ttp) REVERT: n 131 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8097 (mp) REVERT: n 159 VAL cc_start: 0.8965 (p) cc_final: 0.8687 (m) outliers start: 11 outliers final: 9 residues processed: 190 average time/residue: 0.2685 time to fit residues: 77.1277 Evaluate side-chains 194 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 183 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain c residue 80 PHE Chi-restraints excluded: chain c residue 150 ILE Chi-restraints excluded: chain d residue 251 LEU Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain h residue 129 MET Chi-restraints excluded: chain h residue 151 ASN Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain n residue 131 LEU Chi-restraints excluded: chain o residue 89 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 65 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 191 optimal weight: 0.0060 chunk 164 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 208 optimal weight: 0.9980 chunk 210 optimal weight: 0.5980 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** n 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.145657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.101480 restraints weight = 51039.600| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.49 r_work: 0.3192 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17500 Z= 0.147 Angle : 0.470 7.465 23787 Z= 0.258 Chirality : 0.036 0.137 2900 Planarity : 0.003 0.058 2969 Dihedral : 3.875 36.673 2496 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.63 % Allowed : 8.67 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.31 (0.17), residues: 2313 helix: 2.08 (0.12), residues: 1741 sheet: -1.23 (0.90), residues: 29 loop : -0.07 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 57 TYR 0.013 0.001 TYR m 142 PHE 0.024 0.001 PHE B 93 TRP 0.007 0.001 TRP d 312 HIS 0.012 0.001 HIS F 56 Details of bonding type rmsd covalent geometry : bond 0.00293 (17500) covalent geometry : angle 0.47018 (23787) hydrogen bonds : bond 0.04816 ( 1433) hydrogen bonds : angle 4.26120 ( 4248) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6488.93 seconds wall clock time: 110 minutes 41.84 seconds (6641.84 seconds total)