Starting phenix.real_space_refine on Sun Jun 29 07:51:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eat_27985/06_2025/8eat_27985.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eat_27985/06_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_27985/06_2025/8eat_27985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eat_27985/06_2025/8eat_27985.map" model { file = "/net/cci-nas-00/data/ceres_data/8eat_27985/06_2025/8eat_27985.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eat_27985/06_2025/8eat_27985.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.194 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 3} 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: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 2} 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: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} 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: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 5} 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: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP: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: 15.10, per 1000 atoms: 0.44 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: 9.27 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 2.53 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: 13.71 Time building geometry restraints manager: 10.99 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: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.570 Extract box with map and model: 1.210 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 70.040 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.300 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (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 TRP 0.035 0.002 TRP c 77 HIS 0.003 0.001 HIS d 78 PHE 0.038 0.001 PHE d 192 TYR 0.023 0.001 TYR d 185 ARG 0.005 0.000 ARG d 181 Details of bonding type rmsd hydrogen bonds : bond 0.16690 ( 1433) hydrogen bonds : angle 8.23520 ( 4248) covalent geometry : bond 0.00409 (17500) covalent geometry : angle 0.54353 (23787) *********************** 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 : 2.721 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: 0.7503 time to fit residues: 255.3838 Evaluate side-chains 198 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 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 = 0.3821 r_free = 0.3821 target = 0.145646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.100836 restraints weight = 50114.259| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.51 r_work: 0.3125 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.0961 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= 0.201 Angle : 0.540 7.111 23787 Z= 0.299 Chirality : 0.038 0.133 2900 Planarity : 0.004 0.088 2969 Dihedral : 4.222 52.867 2496 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.46 % Allowed : 3.76 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.17), residues: 2313 helix: 1.48 (0.12), residues: 1733 sheet: -1.00 (0.88), residues: 30 loop : -0.24 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 77 HIS 0.003 0.001 HIS B 38 PHE 0.029 0.001 PHE c 80 TYR 0.013 0.001 TYR A 50 ARG 0.006 0.000 ARG F 80 Details of bonding type rmsd hydrogen bonds : bond 0.06052 ( 1433) hydrogen bonds : angle 5.04329 ( 4248) covalent geometry : bond 0.00413 (17500) covalent geometry : angle 0.53982 (23787) *********************** 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 211 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 203 time to evaluate : 2.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 274 GLU cc_start: 0.6675 (tp30) cc_final: 0.6376 (tt0) REVERT: n 129 MET cc_start: 0.7150 (ttp) cc_final: 0.6696 (ttp) outliers start: 8 outliers final: 6 residues processed: 207 average time/residue: 0.6890 time to fit residues: 217.7056 Evaluate side-chains 202 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 196 time to evaluate : 2.385 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 174 optimal weight: 1.9990 chunk 70 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 15 optimal weight: 40.0000 chunk 164 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN l 121 GLN o 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.143987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.098987 restraints weight = 50774.606| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.51 r_work: 0.3115 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17500 Z= 0.213 Angle : 0.514 5.583 23787 Z= 0.286 Chirality : 0.038 0.131 2900 Planarity : 0.004 0.089 2969 Dihedral : 4.204 52.413 2496 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.57 % Allowed : 4.79 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.17), residues: 2313 helix: 1.53 (0.12), residues: 1740 sheet: -1.12 (0.88), residues: 30 loop : -0.19 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 77 HIS 0.002 0.001 HIS B 38 PHE 0.029 0.001 PHE c 80 TYR 0.011 0.001 TYR o 127 ARG 0.002 0.000 ARG j 153 Details of bonding type rmsd hydrogen bonds : bond 0.05706 ( 1433) hydrogen bonds : angle 4.79858 ( 4248) covalent geometry : bond 0.00452 (17500) covalent geometry : angle 0.51430 (23787) *********************** 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: 10 poor density : 198 time to evaluate : 2.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 128 HIS cc_start: 0.5859 (m170) cc_final: 0.5618 (m170) REVERT: g 59 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7989 (mtt) REVERT: j 35 SER cc_start: 0.8802 (t) cc_final: 0.8429 (m) REVERT: n 129 MET cc_start: 0.7062 (ttp) cc_final: 0.6727 (ttp) outliers start: 10 outliers final: 7 residues processed: 203 average time/residue: 0.6874 time to fit residues: 215.5797 Evaluate side-chains 198 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 190 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain b residue 247 LEU 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 173 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 218 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 196 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.141590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.095859 restraints weight = 51380.001| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.59 r_work: 0.3101 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17500 Z= 0.214 Angle : 0.507 5.435 23787 Z= 0.281 Chirality : 0.037 0.130 2900 Planarity : 0.004 0.075 2969 Dihedral : 4.190 51.540 2496 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.63 % Allowed : 5.88 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.17), residues: 2313 helix: 1.54 (0.12), residues: 1742 sheet: -1.17 (0.87), residues: 30 loop : -0.18 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP c 77 HIS 0.003 0.001 HIS o 129 PHE 0.028 0.001 PHE c 80 TYR 0.011 0.001 TYR A 50 ARG 0.003 0.000 ARG F 80 Details of bonding type rmsd hydrogen bonds : bond 0.05467 ( 1433) hydrogen bonds : angle 4.67162 ( 4248) covalent geometry : bond 0.00458 (17500) covalent geometry : angle 0.50695 (23787) *********************** 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 204 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 193 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 128 HIS cc_start: 0.5970 (m170) cc_final: 0.5761 (m170) REVERT: g 59 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7834 (mtt) REVERT: j 35 SER cc_start: 0.8788 (t) cc_final: 0.8542 (m) REVERT: n 129 MET cc_start: 0.7056 (ttp) cc_final: 0.6745 (ttp) outliers start: 11 outliers final: 9 residues processed: 199 average time/residue: 0.6843 time to fit residues: 207.3852 Evaluate side-chains 198 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 188 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain b residue 247 LEU 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 65 ILE 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 136 optimal weight: 1.9990 chunk 9 optimal weight: 0.0050 chunk 100 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 217 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 56 HIS k 82 GLN o 83 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.145352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.099873 restraints weight = 50616.308| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.58 r_work: 0.3131 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1631 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= 0.157 Angle : 0.473 5.259 23787 Z= 0.260 Chirality : 0.036 0.128 2900 Planarity : 0.004 0.064 2969 Dihedral : 4.064 47.872 2496 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.63 % Allowed : 6.56 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.17), residues: 2313 helix: 1.78 (0.12), residues: 1739 sheet: -1.18 (0.86), residues: 30 loop : -0.12 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP d 312 HIS 0.002 0.001 HIS B 82 PHE 0.025 0.001 PHE c 80 TYR 0.010 0.001 TYR A 50 ARG 0.002 0.000 ARG F 80 Details of bonding type rmsd hydrogen bonds : bond 0.05112 ( 1433) hydrogen bonds : angle 4.47319 ( 4248) covalent geometry : bond 0.00316 (17500) covalent geometry : angle 0.47255 (23787) *********************** 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 209 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 198 time to evaluate : 2.536 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: B 1 MET cc_start: 0.7988 (tpt) cc_final: 0.7216 (tpp) REVERT: c 80 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.8780 (p90) REVERT: d 179 ILE cc_start: 0.7791 (mm) cc_final: 0.7434 (mm) REVERT: d 199 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7647 (mm-30) REVERT: d 223 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7366 (mp) REVERT: g 59 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7613 (mtt) REVERT: l 50 LEU cc_start: 0.8331 (tp) cc_final: 0.8073 (tt) REVERT: n 129 MET cc_start: 0.7052 (ttp) cc_final: 0.6745 (ttp) outliers start: 11 outliers final: 5 residues processed: 205 average time/residue: 0.6781 time to fit residues: 213.0772 Evaluate side-chains 199 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 191 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 151 ASN Chi-restraints excluded: chain j residue 113 ASP 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 154 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 67 optimal weight: 9.9990 chunk 97 optimal weight: 0.5980 chunk 146 optimal weight: 0.3980 chunk 63 optimal weight: 0.9980 chunk 176 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 56 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.144200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.098863 restraints weight = 50517.043| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.57 r_work: 0.3138 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17500 Z= 0.142 Angle : 0.459 6.153 23787 Z= 0.253 Chirality : 0.036 0.134 2900 Planarity : 0.003 0.062 2969 Dihedral : 3.930 42.608 2496 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.80 % Allowed : 7.13 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.17), residues: 2313 helix: 1.97 (0.12), residues: 1738 sheet: -1.23 (0.86), residues: 30 loop : -0.04 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP d 312 HIS 0.003 0.001 HIS d 128 PHE 0.023 0.001 PHE B 93 TYR 0.012 0.001 TYR d 289 ARG 0.004 0.000 ARG A 57 Details of bonding type rmsd hydrogen bonds : bond 0.04896 ( 1433) hydrogen bonds : angle 4.32924 ( 4248) covalent geometry : bond 0.00279 (17500) covalent geometry : angle 0.45867 (23787) *********************** 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 213 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 2.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLN cc_start: 0.4199 (mm-40) cc_final: 0.3885 (mm-40) REVERT: B 1 MET cc_start: 0.7963 (tpt) cc_final: 0.7241 (tpp) REVERT: c 80 PHE cc_start: 0.8996 (OUTLIER) cc_final: 0.8723 (p90) REVERT: d 179 ILE cc_start: 0.7811 (mm) cc_final: 0.7457 (mm) REVERT: d 223 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7345 (mp) REVERT: g 59 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7479 (mtt) REVERT: l 50 LEU cc_start: 0.8265 (tp) cc_final: 0.8047 (tt) REVERT: n 129 MET cc_start: 0.7083 (ttp) cc_final: 0.6785 (ttp) outliers start: 14 outliers final: 7 residues processed: 206 average time/residue: 0.6931 time to fit residues: 215.8166 Evaluate side-chains 205 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 195 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 23 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 164 optimal weight: 0.0570 chunk 155 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 165 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 178 optimal weight: 0.0980 chunk 213 optimal weight: 0.9990 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 56 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.145374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.099897 restraints weight = 50632.004| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.58 r_work: 0.3168 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17500 Z= 0.128 Angle : 0.452 6.326 23787 Z= 0.248 Chirality : 0.036 0.144 2900 Planarity : 0.003 0.059 2969 Dihedral : 3.848 38.184 2496 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.57 % Allowed : 7.70 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.17), residues: 2313 helix: 2.14 (0.12), residues: 1737 sheet: -1.12 (0.88), residues: 29 loop : 0.05 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP d 312 HIS 0.002 0.001 HIS d 128 PHE 0.021 0.001 PHE c 80 TYR 0.010 0.001 TYR A 50 ARG 0.003 0.000 ARG F 111 Details of bonding type rmsd hydrogen bonds : bond 0.04771 ( 1433) hydrogen bonds : angle 4.24096 ( 4248) covalent geometry : bond 0.00243 (17500) covalent geometry : angle 0.45164 (23787) *********************** 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: 10 poor density : 197 time to evaluate : 3.169 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: A 128 GLN cc_start: 0.4140 (mm-40) cc_final: 0.3925 (mm-40) REVERT: B 1 MET cc_start: 0.7947 (tpt) cc_final: 0.7214 (tpp) REVERT: c 80 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8704 (p90) REVERT: d 179 ILE cc_start: 0.7767 (mm) cc_final: 0.7421 (mm) REVERT: j 3 GLU cc_start: 0.7944 (pt0) cc_final: 0.7570 (tt0) REVERT: n 129 MET cc_start: 0.7065 (ttp) cc_final: 0.6782 (ttp) REVERT: n 159 VAL cc_start: 0.8905 (p) cc_final: 0.8604 (m) outliers start: 10 outliers final: 8 residues processed: 202 average time/residue: 0.8662 time to fit residues: 271.6796 Evaluate side-chains 200 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 191 time to evaluate : 3.306 ------------------------------------------------------------------------------- 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 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 8 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 56 HIS k 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.143508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.098898 restraints weight = 51650.304| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.50 r_work: 0.3158 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17500 Z= 0.227 Angle : 0.501 5.307 23787 Z= 0.278 Chirality : 0.038 0.139 2900 Planarity : 0.004 0.056 2969 Dihedral : 3.979 39.915 2496 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.63 % Allowed : 8.16 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.17), residues: 2313 helix: 1.87 (0.12), residues: 1742 sheet: -1.14 (0.90), residues: 29 loop : -0.08 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP c 77 HIS 0.004 0.001 HIS F 72 PHE 0.027 0.001 PHE c 80 TYR 0.010 0.001 TYR d 51 ARG 0.003 0.000 ARG d 321 Details of bonding type rmsd hydrogen bonds : bond 0.05185 ( 1433) hydrogen bonds : angle 4.43621 ( 4248) covalent geometry : bond 0.00495 (17500) covalent geometry : angle 0.50077 (23787) *********************** 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 202 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 191 time to evaluate : 2.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLN cc_start: 0.4271 (mm-40) cc_final: 0.3970 (mm-40) REVERT: c 80 PHE cc_start: 0.9157 (OUTLIER) cc_final: 0.8951 (p90) REVERT: d 179 ILE cc_start: 0.7961 (mm) cc_final: 0.7602 (mm) REVERT: d 223 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7587 (mp) REVERT: g 59 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7866 (mtt) REVERT: n 129 MET cc_start: 0.7344 (ttp) cc_final: 0.7035 (ttp) REVERT: n 159 VAL cc_start: 0.9026 (p) cc_final: 0.8747 (m) outliers start: 11 outliers final: 8 residues processed: 197 average time/residue: 0.7020 time to fit residues: 207.4852 Evaluate side-chains 198 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 187 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 61 optimal weight: 0.9980 chunk 211 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 139 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 56 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.146223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.101301 restraints weight = 50341.120| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.51 r_work: 0.3158 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17500 Z= 0.140 Angle : 0.460 5.511 23787 Z= 0.253 Chirality : 0.036 0.129 2900 Planarity : 0.003 0.056 2969 Dihedral : 3.869 37.215 2496 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.63 % Allowed : 8.39 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.17), residues: 2313 helix: 2.07 (0.12), residues: 1741 sheet: -1.11 (0.91), residues: 29 loop : -0.02 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP d 312 HIS 0.002 0.001 HIS F 56 PHE 0.021 0.001 PHE c 80 TYR 0.011 0.001 TYR d 289 ARG 0.003 0.000 ARG F 111 Details of bonding type rmsd hydrogen bonds : bond 0.04849 ( 1433) hydrogen bonds : angle 4.27505 ( 4248) covalent geometry : bond 0.00275 (17500) covalent geometry : angle 0.46032 (23787) *********************** 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 205 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 194 time to evaluate : 2.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLN cc_start: 0.4197 (mm-40) cc_final: 0.3977 (mm-40) REVERT: B 1 MET cc_start: 0.7979 (tpt) cc_final: 0.7386 (tpp) REVERT: F 102 ASP cc_start: 0.8395 (t0) cc_final: 0.8104 (t0) REVERT: c 80 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8823 (p90) REVERT: d 179 ILE cc_start: 0.7840 (mm) cc_final: 0.7500 (mm) REVERT: d 223 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7445 (mp) REVERT: j 3 GLU cc_start: 0.7913 (pt0) cc_final: 0.7482 (tt0) REVERT: m 5 CYS cc_start: 0.8042 (p) cc_final: 0.7775 (p) REVERT: n 129 MET cc_start: 0.7119 (ttp) cc_final: 0.6820 (ttp) REVERT: n 131 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7986 (mp) REVERT: n 159 VAL cc_start: 0.8898 (p) cc_final: 0.8615 (m) outliers start: 11 outliers final: 6 residues processed: 200 average time/residue: 0.6808 time to fit residues: 207.9580 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 : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 214 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 48 optimal weight: 0.0970 chunk 0 optimal weight: 20.0000 chunk 145 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 119 optimal weight: 0.0870 chunk 52 optimal weight: 1.9990 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 56 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.143499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.098059 restraints weight = 50556.149| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.58 r_work: 0.3136 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17500 Z= 0.162 Angle : 0.468 5.499 23787 Z= 0.258 Chirality : 0.036 0.130 2900 Planarity : 0.003 0.055 2969 Dihedral : 3.853 35.419 2496 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.51 % Allowed : 8.73 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.17), residues: 2313 helix: 2.05 (0.12), residues: 1748 sheet: -1.15 (0.91), residues: 29 loop : -0.02 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP d 312 HIS 0.003 0.001 HIS F 72 PHE 0.023 0.001 PHE c 80 TYR 0.009 0.001 TYR A 50 ARG 0.003 0.000 ARG F 111 Details of bonding type rmsd hydrogen bonds : bond 0.04886 ( 1433) hydrogen bonds : angle 4.28120 ( 4248) covalent geometry : bond 0.00334 (17500) covalent geometry : angle 0.46781 (23787) ********************** 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 201 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 192 time to evaluate : 4.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLN cc_start: 0.4202 (mm-40) cc_final: 0.3979 (mm-40) REVERT: B 1 MET cc_start: 0.7904 (tpt) cc_final: 0.7318 (tpp) REVERT: F 102 ASP cc_start: 0.8380 (t0) cc_final: 0.8093 (t0) REVERT: c 80 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8809 (p90) REVERT: d 179 ILE cc_start: 0.7803 (mm) cc_final: 0.7456 (mm) REVERT: d 223 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7455 (mp) REVERT: j 3 GLU cc_start: 0.7934 (pt0) cc_final: 0.7491 (tt0) REVERT: n 129 MET cc_start: 0.7116 (ttp) cc_final: 0.6822 (ttp) REVERT: n 131 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7966 (mp) REVERT: n 159 VAL cc_start: 0.8862 (p) cc_final: 0.8578 (m) outliers start: 9 outliers final: 6 residues processed: 198 average time/residue: 0.8409 time to fit residues: 262.2141 Evaluate side-chains 199 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 190 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 38 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 56 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.145737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.100829 restraints weight = 50263.464| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.51 r_work: 0.3131 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17500 Z= 0.190 Angle : 0.485 5.639 23787 Z= 0.267 Chirality : 0.037 0.132 2900 Planarity : 0.003 0.054 2969 Dihedral : 3.898 35.738 2496 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.63 % Allowed : 8.78 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.17), residues: 2313 helix: 1.96 (0.12), residues: 1747 sheet: -1.21 (0.91), residues: 29 loop : -0.08 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP d 312 HIS 0.003 0.001 HIS F 72 PHE 0.025 0.001 PHE c 80 TYR 0.008 0.001 TYR o 127 ARG 0.003 0.000 ARG F 111 Details of bonding type rmsd hydrogen bonds : bond 0.05001 ( 1433) hydrogen bonds : angle 4.33642 ( 4248) covalent geometry : bond 0.00403 (17500) covalent geometry : angle 0.48474 (23787) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17530.95 seconds wall clock time: 308 minutes 49.25 seconds (18529.25 seconds total)