Starting phenix.real_space_refine on Tue Aug 26 02:04:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rmm_19364/08_2025/8rmm_19364.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rmm_19364/08_2025/8rmm_19364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rmm_19364/08_2025/8rmm_19364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rmm_19364/08_2025/8rmm_19364.map" model { file = "/net/cci-nas-00/data/ceres_data/8rmm_19364/08_2025/8rmm_19364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rmm_19364/08_2025/8rmm_19364.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.036 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 P 6 5.49 5 S 158 5.16 5 C 21092 2.51 5 N 5695 2.21 5 O 5937 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32888 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2053 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 11, 'TRANS': 251} Chain breaks: 1 Chain: "L" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "B" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2053 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 11, 'TRANS': 251} Chain breaks: 1 Chain: "M" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "C" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2177 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 14, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 6, 'ASN:plan1': 4, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 51 Chain: "D" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2298 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 15, 'TRANS': 272} Chain breaks: 1 Chain: "O" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "E" Number of atoms: 2313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2313 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 15, 'TRANS': 274} Chain breaks: 1 Chain: "P" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "F" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2298 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 15, 'TRANS': 272} Chain breaks: 1 Chain: "Q" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "G" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2298 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 15, 'TRANS': 272} Chain breaks: 1 Chain: "R" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "H" Number of atoms: 2289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2289 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 15, 'TRANS': 271} Chain breaks: 1 Chain: "S" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "I" Number of atoms: 2289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2289 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 15, 'TRANS': 271} Chain breaks: 1 Chain: "T" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "J" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1778 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 11, 'TRANS': 218} Chain breaks: 3 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ASP:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 63 Chain: "K" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1871 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 8, 'TRANS': 231} Chain breaks: 1 Chain: "U" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.56, per 1000 atoms: 0.26 Number of scatterers: 32888 At special positions: 0 Unit cell: (157.542, 197.904, 187.488, 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 158 16.00 P 6 15.00 O 5937 8.00 N 5695 7.00 C 21092 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 131 " distance=2.03 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 131 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 130 " distance=2.03 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS D 46 " - pdb=" SG CYS D 130 " distance=2.03 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 162 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 130 " distance=2.03 Simple disulfide: pdb=" SG CYS E 48 " - pdb=" SG CYS E 162 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 46 " - pdb=" SG CYS F 130 " distance=2.03 Simple disulfide: pdb=" SG CYS F 48 " - pdb=" SG CYS F 162 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 130 " distance=2.03 Simple disulfide: pdb=" SG CYS G 48 " - pdb=" SG CYS G 162 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 46 " - pdb=" SG CYS H 130 " distance=2.03 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 162 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS I 46 " - pdb=" SG CYS I 130 " distance=2.03 Simple disulfide: pdb=" SG CYS I 48 " - pdb=" SG CYS I 162 " distance=2.03 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS T 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 48 " - pdb=" SG CYS J 162 " distance=2.03 Simple disulfide: pdb=" SG CYS K 41 " - pdb=" SG CYS K 131 " distance=2.03 Simple disulfide: pdb=" SG CYS K 43 " - pdb=" SG CYS K 162 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.2 microseconds 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7778 Finding SS restraints... Secondary structure from input PDB file: 163 helices and 33 sheets defined 56.7% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 Processing helix chain 'A' and resid 15 through 38 removed outlier: 4.190A pdb=" N ILE A 19 " --> pdb=" O ASN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 70 Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.801A pdb=" N TRP A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 107 removed outlier: 4.023A pdb=" N ILE A 107 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 126 removed outlier: 4.503A pdb=" N ALA A 114 " --> pdb=" O ARG A 110 " (cutoff:3.500A) Proline residue: A 115 - end of helix Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 151 through 160 removed outlier: 3.598A pdb=" N GLU A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 208 Processing helix chain 'A' and resid 216 through 253 removed outlier: 3.554A pdb=" N TYR A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 273 removed outlier: 4.106A pdb=" N TRP A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS A 273 " --> pdb=" O CYS A 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 268 through 273' Processing helix chain 'A' and resid 274 through 277 removed outlier: 3.772A pdb=" N VAL A 277 " --> pdb=" O ASP A 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 274 through 277' Processing helix chain 'L' and resid 87 through 91 Processing helix chain 'B' and resid 6 through 15 Processing helix chain 'B' and resid 15 through 38 removed outlier: 3.888A pdb=" N ILE B 19 " --> pdb=" O ASN B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 70 removed outlier: 3.633A pdb=" N GLY B 52 " --> pdb=" O ASN B 48 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 72 through 82 removed outlier: 3.798A pdb=" N THR B 76 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 126 removed outlier: 3.553A pdb=" N GLY B 109 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ARG B 110 " --> pdb=" O SER B 106 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA B 114 " --> pdb=" O ARG B 110 " (cutoff:3.500A) Proline residue: B 115 - end of helix Processing helix chain 'B' and resid 126 through 133 Processing helix chain 'B' and resid 151 through 160 Processing helix chain 'B' and resid 170 through 208 Processing helix chain 'B' and resid 214 through 252 removed outlier: 4.054A pdb=" N CYS B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 275 removed outlier: 4.026A pdb=" N TRP B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS B 273 " --> pdb=" O CYS B 269 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP B 274 " --> pdb=" O GLN B 270 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE B 275 " --> pdb=" O ASP B 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 268 through 275' Processing helix chain 'M' and resid 62 through 65 Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'C' and resid 20 through 43 Processing helix chain 'C' and resid 52 through 60 Processing helix chain 'C' and resid 61 through 76 removed outlier: 3.536A pdb=" N ASN C 76 " --> pdb=" O GLY C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 89 removed outlier: 4.517A pdb=" N TRP C 80 " --> pdb=" O ASN C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 111 removed outlier: 3.569A pdb=" N LEU C 102 " --> pdb=" O PRO C 98 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 107 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY C 108 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 Processing helix chain 'C' and resid 125 through 133 Processing helix chain 'C' and resid 137 through 141 removed outlier: 3.784A pdb=" N LEU C 141 " --> pdb=" O PRO C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 159 Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'C' and resid 169 through 209 removed outlier: 3.989A pdb=" N GLU C 175 " --> pdb=" O ASP C 171 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 252 Processing helix chain 'C' and resid 257 through 267 Processing helix chain 'C' and resid 274 through 281 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'D' and resid 38 through 42 Processing helix chain 'D' and resid 52 through 76 removed outlier: 3.512A pdb=" N VAL D 63 " --> pdb=" O ALA D 59 " (cutoff:3.500A) Proline residue: D 64 - end of helix Processing helix chain 'D' and resid 79 through 90 removed outlier: 3.570A pdb=" N VAL D 83 " --> pdb=" O THR D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 111 removed outlier: 3.742A pdb=" N THR D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 125 removed outlier: 3.841A pdb=" N ILE D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 130 Processing helix chain 'D' and resid 137 through 141 Processing helix chain 'D' and resid 152 through 158 removed outlier: 3.503A pdb=" N ILE D 156 " --> pdb=" O HIS D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 166 through 168 No H-bonds generated for 'chain 'D' and resid 166 through 168' Processing helix chain 'D' and resid 169 through 210 removed outlier: 3.541A pdb=" N GLU D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE D 200 " --> pdb=" O ALA D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 252 removed outlier: 3.543A pdb=" N ASN D 226 " --> pdb=" O GLN D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.665A pdb=" N GLU D 262 " --> pdb=" O LYS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 280 Processing helix chain 'D' and resid 297 through 304 Processing helix chain 'D' and resid 323 through 329 Processing helix chain 'O' and resid 87 through 91 Processing helix chain 'E' and resid 36 through 42 removed outlier: 3.603A pdb=" N SER E 40 " --> pdb=" O GLN E 36 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL E 41 " --> pdb=" O GLU E 37 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 36 through 42' Processing helix chain 'E' and resid 52 through 76 Proline residue: E 64 - end of helix removed outlier: 3.528A pdb=" N ASN E 76 " --> pdb=" O GLY E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 89 Processing helix chain 'E' and resid 95 through 111 removed outlier: 3.583A pdb=" N THR E 99 " --> pdb=" O SER E 95 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU E 101 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER E 105 " --> pdb=" O LEU E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 125 removed outlier: 3.755A pdb=" N ILE E 120 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU E 122 " --> pdb=" O SER E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 133 Processing helix chain 'E' and resid 134 through 136 No H-bonds generated for 'chain 'E' and resid 134 through 136' Processing helix chain 'E' and resid 137 through 141 Processing helix chain 'E' and resid 152 through 159 removed outlier: 3.760A pdb=" N ILE E 156 " --> pdb=" O HIS E 152 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 163 Processing helix chain 'E' and resid 166 through 168 No H-bonds generated for 'chain 'E' and resid 166 through 168' Processing helix chain 'E' and resid 169 through 210 removed outlier: 3.652A pdb=" N ARG E 181 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE E 200 " --> pdb=" O ALA E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 252 removed outlier: 3.953A pdb=" N GLN E 232 " --> pdb=" O ASP E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 267 removed outlier: 3.840A pdb=" N GLU E 262 " --> pdb=" O LYS E 258 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA E 265 " --> pdb=" O GLU E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 280 Processing helix chain 'E' and resid 297 through 304 Processing helix chain 'E' and resid 323 through 329 removed outlier: 3.947A pdb=" N PHE E 329 " --> pdb=" O LEU E 325 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 91 Processing helix chain 'F' and resid 38 through 42 Processing helix chain 'F' and resid 52 through 76 Proline residue: F 64 - end of helix Processing helix chain 'F' and resid 79 through 90 removed outlier: 3.515A pdb=" N ARG F 89 " --> pdb=" O GLU F 85 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG F 90 " --> pdb=" O CYS F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 111 removed outlier: 3.643A pdb=" N THR F 99 " --> pdb=" O SER F 95 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU F 101 " --> pdb=" O ALA F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 125 removed outlier: 3.775A pdb=" N ILE F 120 " --> pdb=" O THR F 116 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU F 122 " --> pdb=" O SER F 118 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY F 125 " --> pdb=" O SER F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 132 removed outlier: 3.660A pdb=" N ALA F 131 " --> pdb=" O ALA F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 141 Processing helix chain 'F' and resid 152 through 159 removed outlier: 3.645A pdb=" N ARG F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 163 Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 169 through 210 removed outlier: 3.635A pdb=" N PHE F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 252 removed outlier: 3.624A pdb=" N ASN F 226 " --> pdb=" O GLN F 222 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN F 229 " --> pdb=" O ALA F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 267 removed outlier: 3.523A pdb=" N LEU F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 280 Processing helix chain 'F' and resid 297 through 304 Processing helix chain 'F' and resid 323 through 329 removed outlier: 3.513A pdb=" N LEU F 328 " --> pdb=" O ALA F 324 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE F 329 " --> pdb=" O LEU F 325 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 91 Processing helix chain 'G' and resid 38 through 42 Processing helix chain 'G' and resid 52 through 76 removed outlier: 3.504A pdb=" N VAL G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) Proline residue: G 64 - end of helix Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.594A pdb=" N ARG G 89 " --> pdb=" O GLU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 111 removed outlier: 3.822A pdb=" N THR G 99 " --> pdb=" O SER G 95 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU G 101 " --> pdb=" O ALA G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 125 removed outlier: 3.656A pdb=" N ILE G 120 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY G 125 " --> pdb=" O SER G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 132 removed outlier: 3.527A pdb=" N ALA G 131 " --> pdb=" O ALA G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 136 Processing helix chain 'G' and resid 152 through 159 removed outlier: 3.604A pdb=" N ARG G 159 " --> pdb=" O GLU G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 163 Processing helix chain 'G' and resid 166 through 168 No H-bonds generated for 'chain 'G' and resid 166 through 168' Processing helix chain 'G' and resid 169 through 210 Processing helix chain 'G' and resid 215 through 252 removed outlier: 3.567A pdb=" N ASN G 226 " --> pdb=" O GLN G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 267 removed outlier: 3.926A pdb=" N GLU G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 274 through 280 Processing helix chain 'G' and resid 297 through 304 Processing helix chain 'G' and resid 323 through 329 removed outlier: 3.588A pdb=" N LEU G 328 " --> pdb=" O ALA G 324 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE G 329 " --> pdb=" O LEU G 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 91 Processing helix chain 'H' and resid 52 through 76 Proline residue: H 64 - end of helix Processing helix chain 'H' and resid 79 through 89 removed outlier: 3.578A pdb=" N ARG H 89 " --> pdb=" O GLU H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 111 removed outlier: 3.884A pdb=" N THR H 99 " --> pdb=" O SER H 95 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU H 102 " --> pdb=" O PRO H 98 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER H 105 " --> pdb=" O LEU H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 125 removed outlier: 3.769A pdb=" N ILE H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 132 Processing helix chain 'H' and resid 133 through 136 removed outlier: 3.693A pdb=" N VAL H 136 " --> pdb=" O SER H 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 133 through 136' Processing helix chain 'H' and resid 152 through 159 removed outlier: 3.635A pdb=" N ARG H 159 " --> pdb=" O GLU H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'H' and resid 169 through 210 removed outlier: 3.922A pdb=" N ARG H 181 " --> pdb=" O SER H 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 252 removed outlier: 3.608A pdb=" N ALA H 218 " --> pdb=" O TYR H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 267 removed outlier: 3.574A pdb=" N GLU H 262 " --> pdb=" O LYS H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 274 through 280 Processing helix chain 'H' and resid 297 through 304 Processing helix chain 'H' and resid 323 through 328 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.547A pdb=" N THR S 91 " --> pdb=" O PRO S 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 76 removed outlier: 3.537A pdb=" N TYR I 56 " --> pdb=" O ARG I 52 " (cutoff:3.500A) Proline residue: I 64 - end of helix removed outlier: 3.550A pdb=" N GLY I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 90 removed outlier: 3.508A pdb=" N ASN I 81 " --> pdb=" O ASN I 77 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG I 90 " --> pdb=" O CYS I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 111 removed outlier: 3.902A pdb=" N THR I 99 " --> pdb=" O SER I 95 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU I 101 " --> pdb=" O ALA I 97 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU I 102 " --> pdb=" O PRO I 98 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER I 104 " --> pdb=" O PHE I 100 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU I 107 " --> pdb=" O LEU I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 125 removed outlier: 4.205A pdb=" N ILE I 120 " --> pdb=" O THR I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 132 Processing helix chain 'I' and resid 137 through 141 Processing helix chain 'I' and resid 152 through 159 Processing helix chain 'I' and resid 166 through 168 No H-bonds generated for 'chain 'I' and resid 166 through 168' Processing helix chain 'I' and resid 169 through 210 removed outlier: 3.517A pdb=" N TYR I 182 " --> pdb=" O ARG I 178 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS I 207 " --> pdb=" O LYS I 203 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR I 208 " --> pdb=" O CYS I 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 213 through 252 removed outlier: 3.558A pdb=" N ASP I 228 " --> pdb=" O ARG I 224 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLN I 229 " --> pdb=" O ALA I 225 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU I 230 " --> pdb=" O ASN I 226 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG I 249 " --> pdb=" O ASN I 245 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE I 250 " --> pdb=" O ASN I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 257 through 267 removed outlier: 4.183A pdb=" N GLU I 262 " --> pdb=" O LYS I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 274 through 280 Processing helix chain 'I' and resid 297 through 304 Processing helix chain 'I' and resid 323 through 328 Processing helix chain 'T' and resid 87 through 91 Processing helix chain 'J' and resid 52 through 76 removed outlier: 3.558A pdb=" N VAL J 63 " --> pdb=" O ALA J 59 " (cutoff:3.500A) Proline residue: J 64 - end of helix Processing helix chain 'J' and resid 77 through 89 removed outlier: 3.653A pdb=" N LEU J 82 " --> pdb=" O HIS J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 110 removed outlier: 3.612A pdb=" N ALA J 110 " --> pdb=" O ILE J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 125 removed outlier: 3.619A pdb=" N VAL J 115 " --> pdb=" O ALA J 111 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG J 124 " --> pdb=" O ILE J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 135 removed outlier: 3.573A pdb=" N VAL J 129 " --> pdb=" O GLY J 125 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS J 130 " --> pdb=" O GLU J 126 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA J 131 " --> pdb=" O ALA J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 159 Processing helix chain 'J' and resid 170 through 210 removed outlier: 3.726A pdb=" N ARG J 179 " --> pdb=" O GLU J 175 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY J 188 " --> pdb=" O SER J 184 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TRP J 189 " --> pdb=" O GLN J 185 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU J 190 " --> pdb=" O LEU J 186 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU J 191 " --> pdb=" O PHE J 187 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS J 203 " --> pdb=" O VAL J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 213 through 252 removed outlier: 3.876A pdb=" N GLN J 229 " --> pdb=" O ALA J 225 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL J 237 " --> pdb=" O ARG J 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 257 through 267 removed outlier: 4.043A pdb=" N GLU J 262 " --> pdb=" O LYS J 258 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU J 263 " --> pdb=" O ASP J 259 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE J 264 " --> pdb=" O ASP J 260 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA J 265 " --> pdb=" O GLU J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 274 through 282 removed outlier: 3.736A pdb=" N ILE J 281 " --> pdb=" O GLN J 277 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR J 282 " --> pdb=" O TRP J 278 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 303 Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 15 through 36 removed outlier: 3.922A pdb=" N ILE K 19 " --> pdb=" O ASN K 15 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER K 36 " --> pdb=" O GLN K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 70 Proline residue: K 59 - end of helix removed outlier: 3.585A pdb=" N LEU K 63 " --> pdb=" O PRO K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 82 removed outlier: 3.510A pdb=" N THR K 76 " --> pdb=" O SER K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 112 removed outlier: 3.822A pdb=" N ARG K 110 " --> pdb=" O SER K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 126 removed outlier: 3.797A pdb=" N LEU K 116 " --> pdb=" O VAL K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 131 Processing helix chain 'K' and resid 151 through 158 Processing helix chain 'K' and resid 170 through 210 removed outlier: 3.704A pdb=" N ARG K 174 " --> pdb=" O VAL K 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 216 through 252 removed outlier: 3.695A pdb=" N GLU K 230 " --> pdb=" O GLN K 226 " (cutoff:3.500A) Processing helix chain 'U' and resid 87 through 91 Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.803A pdb=" N VAL L 5 " --> pdb=" O ALA L 23 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR L 78 " --> pdb=" O ASP L 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 58 through 60 removed outlier: 6.439A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 5 through 7 Processing sheet with id=AA4, first strand: chain 'M' and resid 58 through 60 removed outlier: 6.408A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL M 93 " --> pdb=" O GLN M 39 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 289 through 290 Processing sheet with id=AA6, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'O' and resid 58 through 60 removed outlier: 5.256A pdb=" N GLY O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG O 38 " --> pdb=" O GLY O 47 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA O 99 " --> pdb=" O TYR O 33 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY O 35 " --> pdb=" O ALA O 97 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA O 98 " --> pdb=" O TYR O 115 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN O 105 " --> pdb=" O GLY O 109 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N HIS O 111 " --> pdb=" O GLN O 103 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN O 103 " --> pdb=" O HIS O 111 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 58 through 60 removed outlier: 5.256A pdb=" N GLY O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG O 38 " --> pdb=" O GLY O 47 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA O 99 " --> pdb=" O TYR O 33 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY O 35 " --> pdb=" O ALA O 97 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA O 98 " --> pdb=" O TYR O 115 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TYR O 112 " --> pdb=" O GLU E 317 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N GLU E 317 " --> pdb=" O TYR O 112 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLU O 114 " --> pdb=" O ASN E 315 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ASN E 315 " --> pdb=" O GLU O 114 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 289 through 290 Processing sheet with id=AB1, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'P' and resid 58 through 60 removed outlier: 5.671A pdb=" N GLY P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ARG P 38 " --> pdb=" O GLY P 47 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA P 49 " --> pdb=" O TRP P 36 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS P 96 " --> pdb=" O GLY P 117 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN P 105 " --> pdb=" O GLY P 109 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS P 111 " --> pdb=" O GLN P 103 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 58 through 60 removed outlier: 5.671A pdb=" N GLY P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ARG P 38 " --> pdb=" O GLY P 47 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA P 49 " --> pdb=" O TRP P 36 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS P 96 " --> pdb=" O GLY P 117 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR P 112 " --> pdb=" O GLU F 317 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLU F 317 " --> pdb=" O TYR P 112 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLU P 114 " --> pdb=" O ASN F 315 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASN F 315 " --> pdb=" O GLU P 114 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 289 through 290 Processing sheet with id=AB5, first strand: chain 'Q' and resid 3 through 7 removed outlier: 3.543A pdb=" N THR Q 78 " --> pdb=" O ASP Q 73 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Q' and resid 58 through 60 removed outlier: 6.936A pdb=" N TRP Q 36 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ALA Q 50 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU Q 34 " --> pdb=" O ALA Q 50 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA Q 99 " --> pdb=" O TYR Q 33 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY Q 35 " --> pdb=" O ALA Q 97 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Q' and resid 103 through 105 removed outlier: 3.537A pdb=" N GLN Q 103 " --> pdb=" O HIS Q 111 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN Q 105 " --> pdb=" O GLY Q 109 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 289 through 290 Processing sheet with id=AB9, first strand: chain 'R' and resid 3 through 7 removed outlier: 3.672A pdb=" N GLN R 3 " --> pdb=" O SER R 25 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'R' and resid 58 through 60 removed outlier: 7.048A pdb=" N TRP R 36 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ALA R 50 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU R 34 " --> pdb=" O ALA R 50 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN R 105 " --> pdb=" O GLY R 109 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 58 through 60 removed outlier: 7.048A pdb=" N TRP R 36 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ALA R 50 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU R 34 " --> pdb=" O ALA R 50 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N TYR R 110 " --> pdb=" O MET H 318 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 289 through 290 Processing sheet with id=AC4, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.680A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU S 20 " --> pdb=" O LEU S 81 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.933A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA S 50 " --> pdb=" O LEU S 34 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU S 34 " --> pdb=" O ALA S 50 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY S 35 " --> pdb=" O ALA S 97 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA S 98 " --> pdb=" O TYR S 115 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN S 105 " --> pdb=" O GLY S 109 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN S 103 " --> pdb=" O HIS S 111 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.933A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA S 50 " --> pdb=" O LEU S 34 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU S 34 " --> pdb=" O ALA S 50 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY S 35 " --> pdb=" O ALA S 97 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA S 98 " --> pdb=" O TYR S 115 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR S 112 " --> pdb=" O GLU I 317 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N GLU I 317 " --> pdb=" O TYR S 112 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLU S 114 " --> pdb=" O ASN I 315 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ASN I 315 " --> pdb=" O GLU S 114 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 289 through 290 Processing sheet with id=AC8, first strand: chain 'T' and resid 3 through 7 removed outlier: 3.533A pdb=" N SER T 7 " --> pdb=" O SER T 21 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU T 18 " --> pdb=" O MET T 83 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'T' and resid 58 through 60 removed outlier: 7.099A pdb=" N TRP T 36 " --> pdb=" O VAL T 48 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ALA T 50 " --> pdb=" O LEU T 34 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU T 34 " --> pdb=" O ALA T 50 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY T 35 " --> pdb=" O ALA T 97 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'U' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'U' and resid 10 through 13 removed outlier: 6.429A pdb=" N GLY U 10 " --> pdb=" O THR U 112 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N SER U 114 " --> pdb=" O GLY U 10 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL U 12 " --> pdb=" O SER U 114 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N MET U 34 " --> pdb=" O ALA U 50 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ALA U 50 " --> pdb=" O MET U 34 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TRP U 36 " --> pdb=" O VAL U 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.543A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.936A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ALA N 50 " --> pdb=" O LEU N 34 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU N 34 " --> pdb=" O ALA N 50 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA N 99 " --> pdb=" O TYR N 33 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY N 35 " --> pdb=" O ALA N 97 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.936A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ALA N 50 " --> pdb=" O LEU N 34 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU N 34 " --> pdb=" O ALA N 50 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA N 99 " --> pdb=" O TYR N 33 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY N 35 " --> pdb=" O ALA N 97 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 103 through 105 removed outlier: 3.537A pdb=" N GLN N 103 " --> pdb=" O HIS N 111 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN N 105 " --> pdb=" O GLY N 109 " (cutoff:3.500A) 1958 hydrogen bonds defined for protein. 5562 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: 6.97 Time building geometry restraints manager: 4.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7063 1.33 - 1.46: 8960 1.46 - 1.58: 17440 1.58 - 1.71: 12 1.71 - 1.84: 193 Bond restraints: 33668 Sorted by residual: bond pdb=" N CYS A 43 " pdb=" CA CYS A 43 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.37e-02 5.33e+03 6.93e+00 bond pdb=" CB TYR T 33 " pdb=" CG TYR T 33 " ideal model delta sigma weight residual 1.512 1.569 -0.057 2.20e-02 2.07e+03 6.63e+00 bond pdb=" N ILE O 28 " pdb=" CA ILE O 28 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.35e-02 5.49e+03 6.24e+00 bond pdb=" N GLN E 36 " pdb=" CA GLN E 36 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.11e+00 bond pdb=" N ASP A 169 " pdb=" CA ASP A 169 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.35e-02 5.49e+03 5.99e+00 ... (remaining 33663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 44897 2.20 - 4.41: 666 4.41 - 6.61: 134 6.61 - 8.82: 29 8.82 - 11.02: 9 Bond angle restraints: 45735 Sorted by residual: angle pdb=" N ILE O 28 " pdb=" CA ILE O 28 " pdb=" C ILE O 28 " ideal model delta sigma weight residual 112.29 107.14 5.15 9.40e-01 1.13e+00 3.00e+01 angle pdb=" CA GLN K 238 " pdb=" CB GLN K 238 " pdb=" CG GLN K 238 " ideal model delta sigma weight residual 114.10 121.83 -7.73 2.00e+00 2.50e-01 1.49e+01 angle pdb=" CB GLN S 121 " pdb=" CG GLN S 121 " pdb=" CD GLN S 121 " ideal model delta sigma weight residual 112.60 119.09 -6.49 1.70e+00 3.46e-01 1.46e+01 angle pdb=" CA GLN S 121 " pdb=" CB GLN S 121 " pdb=" CG GLN S 121 " ideal model delta sigma weight residual 114.10 121.69 -7.59 2.00e+00 2.50e-01 1.44e+01 angle pdb=" N TYR F 287 " pdb=" CA TYR F 287 " pdb=" C TYR F 287 " ideal model delta sigma weight residual 111.17 116.51 -5.34 1.41e+00 5.03e-01 1.44e+01 ... (remaining 45730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.83: 19489 34.83 - 69.67: 344 69.67 - 104.50: 34 104.50 - 139.33: 2 139.33 - 174.17: 22 Dihedral angle restraints: 19891 sinusoidal: 7793 harmonic: 12098 Sorted by residual: dihedral pdb=" C2' PLC H 401 " pdb=" C' PLC H 401 " pdb=" C1' PLC H 401 " pdb=" O2 PLC H 401 " ideal model delta sinusoidal sigma weight residual 169.53 -4.64 174.17 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C2' PLC H 401 " pdb=" C' PLC H 401 " pdb=" C1' PLC H 401 " pdb=" O' PLC H 401 " ideal model delta sinusoidal sigma weight residual 348.97 175.32 173.65 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 PLC G 401 " pdb=" C1 PLC G 401 " pdb=" C2 PLC G 401 " pdb=" O3P PLC G 401 " ideal model delta sinusoidal sigma weight residual 67.16 -120.26 -172.58 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 19888 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4421 0.060 - 0.120: 576 0.120 - 0.180: 43 0.180 - 0.240: 6 0.240 - 0.300: 2 Chirality restraints: 5048 Sorted by residual: chirality pdb=" CB VAL K 112 " pdb=" CA VAL K 112 " pdb=" CG1 VAL K 112 " pdb=" CG2 VAL K 112 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB VAL A 112 " pdb=" CA VAL A 112 " pdb=" CG1 VAL A 112 " pdb=" CG2 VAL A 112 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CG LEU K 64 " pdb=" CB LEU K 64 " pdb=" CD1 LEU K 64 " pdb=" CD2 LEU K 64 " both_signs ideal model delta sigma weight residual False -2.59 -2.82 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 5045 not shown) Planarity restraints: 5822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP T 52 " -0.061 2.00e-02 2.50e+03 4.01e-02 4.02e+01 pdb=" CG TRP T 52 " 0.106 2.00e-02 2.50e+03 pdb=" CD1 TRP T 52 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP T 52 " 0.013 2.00e-02 2.50e+03 pdb=" NE1 TRP T 52 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP T 52 " -0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP T 52 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP T 52 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP T 52 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP T 52 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP S 52 " -0.037 2.00e-02 2.50e+03 2.97e-02 2.21e+01 pdb=" CG TRP S 52 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP S 52 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP S 52 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP S 52 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP S 52 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP S 52 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP S 52 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP S 52 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP S 52 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 49 " 0.058 5.00e-02 4.00e+02 8.59e-02 1.18e+01 pdb=" N PRO E 50 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO E 50 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 50 " 0.047 5.00e-02 4.00e+02 ... (remaining 5819 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 538 2.68 - 3.23: 32529 3.23 - 3.79: 50564 3.79 - 4.34: 67783 4.34 - 4.90: 110412 Nonbonded interactions: 261826 Sorted by model distance: nonbonded pdb=" OD1 ASP I 314 " pdb=" N ASN I 315 " model vdw 2.123 3.120 nonbonded pdb=" OH TYR B 142 " pdb=" OE1 GLU B 176 " model vdw 2.195 3.040 nonbonded pdb=" O LEU J 230 " pdb=" OG1 THR J 234 " model vdw 2.210 3.040 nonbonded pdb=" O MET K 144 " pdb=" NH2 ARG U 35 " model vdw 2.215 3.120 nonbonded pdb=" O LEU F 122 " pdb=" OG SER F 184 " model vdw 2.227 3.040 ... (remaining 261821 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 5 through 255) selection = (chain 'B' and resid 5 through 255) selection = chain 'K' } ncs_group { reference = (chain 'C' and resid 38 through 306) selection = (chain 'D' and (resid 38 through 89 or resid 96 through 138 or (resid 139 throug \ h 146 and (name N or name CA or name C or name O or name CB )) or resid 147 thro \ ugh 149 or (resid 150 through 151 and (name N or name CA or name C or name O or \ name CB )) or resid 152 through 162 or (resid 163 through 165 and (name N or nam \ e CA or name C or name O or name CB )) or resid 166 or (resid 167 through 168 an \ d (name N or name CA or name C or name O or name CB )) or resid 169 through 235 \ or (resid 236 and (name N or name CA or name C or name O or name CB )) or resid \ 237 through 256 or (resid 257 through 259 and (name N or name CA or name C or na \ me O or name CB )) or resid 260 or (resid 261 through 262 and (name N or name CA \ or name C or name O or name CB )) or resid 263 through 285 or (resid 286 and (n \ ame N or name CA or name C or name O or name CB )) or resid 287 through 289 or ( \ resid 290 through 291 and (name N or name CA or name C or name O or name CB )) o \ r resid 292 through 306)) selection = (chain 'E' and (resid 38 through 89 or resid 96 through 138 or (resid 139 throug \ h 146 and (name N or name CA or name C or name O or name CB )) or resid 147 thro \ ugh 149 or (resid 150 through 151 and (name N or name CA or name C or name O or \ name CB )) or resid 152 through 162 or (resid 163 through 165 and (name N or nam \ e CA or name C or name O or name CB )) or resid 166 or (resid 167 through 168 an \ d (name N or name CA or name C or name O or name CB )) or resid 169 through 235 \ or (resid 236 and (name N or name CA or name C or name O or name CB )) or resid \ 237 through 256 or (resid 257 through 259 and (name N or name CA or name C or na \ me O or name CB )) or resid 260 or (resid 261 through 262 and (name N or name CA \ or name C or name O or name CB )) or resid 263 through 285 or (resid 286 and (n \ ame N or name CA or name C or name O or name CB )) or resid 287 through 289 or ( \ resid 290 through 291 and (name N or name CA or name C or name O or name CB )) o \ r resid 292 through 306)) selection = (chain 'F' and (resid 38 through 89 or resid 96 through 138 or (resid 139 throug \ h 146 and (name N or name CA or name C or name O or name CB )) or resid 147 thro \ ugh 149 or (resid 150 through 151 and (name N or name CA or name C or name O or \ name CB )) or resid 152 through 162 or (resid 163 through 165 and (name N or nam \ e CA or name C or name O or name CB )) or resid 166 or (resid 167 through 168 an \ d (name N or name CA or name C or name O or name CB )) or resid 169 through 235 \ or (resid 236 and (name N or name CA or name C or name O or name CB )) or resid \ 237 through 256 or (resid 257 through 259 and (name N or name CA or name C or na \ me O or name CB )) or resid 260 or (resid 261 through 262 and (name N or name CA \ or name C or name O or name CB )) or resid 263 through 285 or (resid 286 and (n \ ame N or name CA or name C or name O or name CB )) or resid 287 through 289 or ( \ resid 290 through 291 and (name N or name CA or name C or name O or name CB )) o \ r resid 292 through 306)) selection = (chain 'G' and (resid 38 through 89 or resid 96 through 138 or (resid 139 throug \ h 146 and (name N or name CA or name C or name O or name CB )) or resid 147 thro \ ugh 149 or (resid 150 through 151 and (name N or name CA or name C or name O or \ name CB )) or resid 152 through 162 or (resid 163 through 165 and (name N or nam \ e CA or name C or name O or name CB )) or resid 166 or (resid 167 through 168 an \ d (name N or name CA or name C or name O or name CB )) or resid 169 through 235 \ or (resid 236 and (name N or name CA or name C or name O or name CB )) or resid \ 237 through 256 or (resid 257 through 259 and (name N or name CA or name C or na \ me O or name CB )) or resid 260 or (resid 261 through 262 and (name N or name CA \ or name C or name O or name CB )) or resid 263 through 285 or (resid 286 and (n \ ame N or name CA or name C or name O or name CB )) or resid 287 through 289 or ( \ resid 290 through 291 and (name N or name CA or name C or name O or name CB )) o \ r resid 292 through 306)) selection = (chain 'H' and (resid 38 through 89 or resid 96 through 138 or (resid 139 throug \ h 146 and (name N or name CA or name C or name O or name CB )) or resid 147 thro \ ugh 149 or (resid 150 through 151 and (name N or name CA or name C or name O or \ name CB )) or resid 152 through 162 or (resid 163 through 165 and (name N or nam \ e CA or name C or name O or name CB )) or resid 166 or (resid 167 through 168 an \ d (name N or name CA or name C or name O or name CB )) or resid 169 through 235 \ or (resid 236 and (name N or name CA or name C or name O or name CB )) or resid \ 237 through 256 or (resid 257 through 259 and (name N or name CA or name C or na \ me O or name CB )) or resid 260 or (resid 261 through 262 and (name N or name CA \ or name C or name O or name CB )) or resid 263 through 285 or (resid 286 and (n \ ame N or name CA or name C or name O or name CB )) or resid 287 through 289 or ( \ resid 290 through 291 and (name N or name CA or name C or name O or name CB )) o \ r resid 292 through 306)) selection = (chain 'I' and (resid 38 through 89 or resid 96 through 138 or (resid 139 throug \ h 146 and (name N or name CA or name C or name O or name CB )) or resid 147 thro \ ugh 149 or (resid 150 through 151 and (name N or name CA or name C or name O or \ name CB )) or resid 152 through 162 or (resid 163 through 165 and (name N or nam \ e CA or name C or name O or name CB )) or resid 166 or (resid 167 through 168 an \ d (name N or name CA or name C or name O or name CB )) or resid 169 through 235 \ or (resid 236 and (name N or name CA or name C or name O or name CB )) or resid \ 237 through 256 or (resid 257 through 259 and (name N or name CA or name C or na \ me O or name CB )) or resid 260 or (resid 261 through 262 and (name N or name CA \ or name C or name O or name CB )) or resid 263 through 285 or (resid 286 and (n \ ame N or name CA or name C or name O or name CB )) or resid 287 through 289 or ( \ resid 290 through 291 and (name N or name CA or name C or name O or name CB )) o \ r resid 292 through 306)) } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'U' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.490 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 32.360 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 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 : 0.003 0.070 33696 Z= 0.149 Angle : 0.671 11.024 45791 Z= 0.341 Chirality : 0.041 0.300 5048 Planarity : 0.005 0.100 5822 Dihedral : 14.988 174.169 12029 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.98 % Favored : 96.00 % Rotamer: Outliers : 0.79 % Allowed : 13.47 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.14), residues: 4071 helix: 0.67 (0.12), residues: 2058 sheet: 1.50 (0.20), residues: 622 loop : -0.34 (0.18), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG P 29 TYR 0.040 0.001 TYR U 37 PHE 0.030 0.001 PHE U 97 TRP 0.106 0.002 TRP T 52 HIS 0.008 0.001 HIS D 147 Details of bonding type rmsd covalent geometry : bond 0.00314 (33668) covalent geometry : angle 0.67097 (45735) SS BOND : bond 0.00282 ( 28) SS BOND : angle 0.63167 ( 56) hydrogen bonds : bond 0.24791 ( 1887) hydrogen bonds : angle 7.95395 ( 5562) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 403 time to evaluate : 1.298 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 39 GLN cc_start: 0.0751 (tp40) cc_final: 0.0515 (tp40) REVERT: M 82 GLN cc_start: 0.6426 (tp-100) cc_final: 0.6106 (tp-100) REVERT: C 100 PHE cc_start: 0.4494 (m-80) cc_final: 0.4237 (t80) REVERT: O 72 LEU cc_start: 0.5866 (tp) cc_final: 0.5589 (pt) REVERT: E 101 LEU cc_start: 0.8277 (mt) cc_final: 0.7893 (tt) REVERT: E 109 ARG cc_start: 0.7735 (tmm-80) cc_final: 0.7506 (ttt-90) REVERT: P 118 GLN cc_start: 0.7249 (mp10) cc_final: 0.7004 (mp10) REVERT: R 83 MET cc_start: 0.4724 (mmp) cc_final: 0.4286 (mmp) REVERT: S 60 TYR cc_start: 0.4745 (m-80) cc_final: 0.4518 (m-80) REVERT: S 67 ARG cc_start: 0.5325 (ttm110) cc_final: 0.4413 (mtp85) REVERT: J 134 GLU cc_start: 0.5708 (tt0) cc_final: 0.5093 (mt-10) REVERT: J 288 ARG cc_start: 0.2817 (mmt180) cc_final: 0.2472 (mmt90) REVERT: K 112 VAL cc_start: 0.7536 (p) cc_final: 0.7308 (m) REVERT: K 224 HIS cc_start: 0.2653 (t-90) cc_final: 0.2285 (t-90) REVERT: K 244 MET cc_start: 0.6194 (mmm) cc_final: 0.5849 (mmt) outliers start: 27 outliers final: 10 residues processed: 424 average time/residue: 0.2197 time to fit residues: 150.8502 Evaluate side-chains 352 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 342 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 174 ARG Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 89 GLU Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain H residue 257 ASN Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 185 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 40.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.0070 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 9.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 1.9990 overall best weight: 1.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN C 216 GLN C 279 ASN ** C 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN D 300 HIS P 82 GLN P 111 HIS F 246 ASN Q 1 GLN G 246 ASN G 304 GLN ** R 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 ASN I 81 ASN K 32 GLN K 186 GLN ** K 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN N 111 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.183307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.138816 restraints weight = 64126.331| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.96 r_work: 0.3405 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33696 Z= 0.184 Angle : 0.638 13.001 45791 Z= 0.326 Chirality : 0.041 0.219 5048 Planarity : 0.004 0.057 5822 Dihedral : 13.236 171.454 4813 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.75 % Allowed : 11.63 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.13), residues: 4071 helix: 1.57 (0.11), residues: 2109 sheet: 1.55 (0.20), residues: 605 loop : -0.38 (0.18), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 67 TYR 0.021 0.002 TYR O 33 PHE 0.027 0.002 PHE J 160 TRP 0.032 0.002 TRP R 52 HIS 0.011 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00410 (33668) covalent geometry : angle 0.63779 (45735) SS BOND : bond 0.00335 ( 28) SS BOND : angle 1.02939 ( 56) hydrogen bonds : bond 0.04982 ( 1887) hydrogen bonds : angle 4.74945 ( 5562) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 377 time to evaluate : 1.268 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: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.6319 (mtmt) cc_final: 0.5834 (mptt) REVERT: A 181 HIS cc_start: 0.8179 (m-70) cc_final: 0.7847 (m-70) REVERT: L 70 ILE cc_start: 0.7407 (tp) cc_final: 0.7179 (tp) REVERT: L 80 TYR cc_start: 0.7077 (m-10) cc_final: 0.6840 (m-10) REVERT: B 249 LYS cc_start: 0.6445 (ptpt) cc_final: 0.5952 (tptp) REVERT: M 82 GLN cc_start: 0.7136 (tp-100) cc_final: 0.6867 (tp40) REVERT: C 120 ILE cc_start: 0.9170 (mm) cc_final: 0.8909 (mt) REVERT: O 78 THR cc_start: 0.5539 (t) cc_final: 0.5097 (t) REVERT: O 110 TYR cc_start: 0.8425 (m-80) cc_final: 0.8127 (m-10) REVERT: E 109 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7831 (ttt-90) REVERT: G 137 ASP cc_start: 0.8085 (t0) cc_final: 0.7849 (t0) REVERT: R 33 TYR cc_start: 0.8477 (m-80) cc_final: 0.8189 (m-80) REVERT: R 77 ASN cc_start: 0.7198 (OUTLIER) cc_final: 0.6962 (m-40) REVERT: H 102 LEU cc_start: 0.8488 (tp) cc_final: 0.8279 (tp) REVERT: S 6 GLU cc_start: 0.5872 (pm20) cc_final: 0.5594 (pt0) REVERT: S 67 ARG cc_start: 0.6641 (ttm110) cc_final: 0.6192 (mtp85) REVERT: S 72 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7366 (pp) REVERT: I 259 ASP cc_start: 0.8548 (p0) cc_final: 0.8254 (p0) REVERT: I 329 PHE cc_start: 0.5648 (m-80) cc_final: 0.5383 (m-80) REVERT: J 134 GLU cc_start: 0.6065 (OUTLIER) cc_final: 0.5594 (mt-10) REVERT: J 189 TRP cc_start: 0.7815 (m100) cc_final: 0.7073 (m100) REVERT: J 288 ARG cc_start: 0.2696 (mmt180) cc_final: 0.2115 (mmt90) REVERT: K 142 TYR cc_start: 0.2633 (m-10) cc_final: 0.2311 (m-10) REVERT: K 244 MET cc_start: 0.7229 (mmm) cc_final: 0.6815 (tpt) outliers start: 94 outliers final: 40 residues processed: 446 average time/residue: 0.2125 time to fit residues: 155.4711 Evaluate side-chains 365 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 321 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 59 HIS Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 74 ASN Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 109 ARG Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain Q residue 22 CYS Chi-restraints excluded: chain Q residue 68 PHE Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 182 TYR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain R residue 77 ASN Chi-restraints excluded: chain H residue 169 LEU Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain S residue 95 TYR Chi-restraints excluded: chain I residue 86 CYS Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain K residue 163 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 223 optimal weight: 0.6980 chunk 236 optimal weight: 0.9980 chunk 386 optimal weight: 30.0000 chunk 289 optimal weight: 8.9990 chunk 253 optimal weight: 20.0000 chunk 100 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 315 optimal weight: 8.9990 chunk 302 optimal weight: 0.9990 chunk 390 optimal weight: 0.0470 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 13 GLN R 121 GLN T 121 GLN ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 246 ASN ** K 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.183597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.138200 restraints weight = 63646.878| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.97 r_work: 0.3409 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33696 Z= 0.150 Angle : 0.584 13.127 45791 Z= 0.293 Chirality : 0.040 0.244 5048 Planarity : 0.004 0.032 5822 Dihedral : 12.759 175.390 4796 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.95 % Allowed : 12.42 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.13), residues: 4071 helix: 1.80 (0.11), residues: 2117 sheet: 1.53 (0.21), residues: 584 loop : -0.45 (0.18), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 29 TYR 0.019 0.001 TYR O 33 PHE 0.020 0.001 PHE L 68 TRP 0.035 0.002 TRP U 36 HIS 0.009 0.001 HIS U 33 Details of bonding type rmsd covalent geometry : bond 0.00340 (33668) covalent geometry : angle 0.58310 (45735) SS BOND : bond 0.00294 ( 28) SS BOND : angle 0.88542 ( 56) hydrogen bonds : bond 0.04330 ( 1887) hydrogen bonds : angle 4.35278 ( 5562) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 361 time to evaluate : 1.358 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.6444 (mtmt) cc_final: 0.6011 (mptt) REVERT: A 246 HIS cc_start: 0.7714 (t-90) cc_final: 0.7495 (m90) REVERT: L 70 ILE cc_start: 0.7548 (tp) cc_final: 0.7049 (pt) REVERT: L 80 TYR cc_start: 0.6883 (m-10) cc_final: 0.6549 (m-10) REVERT: B 47 LYS cc_start: 0.5831 (mttt) cc_final: 0.5567 (mtmt) REVERT: B 74 MET cc_start: 0.7650 (mmm) cc_final: 0.7145 (mmm) REVERT: B 249 LYS cc_start: 0.6865 (ptpt) cc_final: 0.6227 (tptp) REVERT: M 82 GLN cc_start: 0.7140 (tp-100) cc_final: 0.6845 (tp40) REVERT: M 83 MET cc_start: 0.6113 (ptt) cc_final: 0.5692 (ptt) REVERT: O 78 THR cc_start: 0.5531 (t) cc_final: 0.5047 (t) REVERT: O 110 TYR cc_start: 0.8413 (m-80) cc_final: 0.8090 (m-10) REVERT: E 109 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7835 (ttt-90) REVERT: Q 29 ARG cc_start: 0.7693 (ptp90) cc_final: 0.7483 (mtm-85) REVERT: Q 57 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.6656 (tt0) REVERT: G 128 TYR cc_start: 0.8658 (t80) cc_final: 0.8369 (t80) REVERT: G 137 ASP cc_start: 0.8096 (t0) cc_final: 0.7745 (t0) REVERT: G 171 ASP cc_start: 0.8049 (p0) cc_final: 0.7766 (m-30) REVERT: G 321 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8341 (pp) REVERT: R 77 ASN cc_start: 0.7290 (m-40) cc_final: 0.7086 (m-40) REVERT: S 6 GLU cc_start: 0.6138 (pm20) cc_final: 0.5161 (tm-30) REVERT: S 7 SER cc_start: 0.6930 (t) cc_final: 0.6474 (m) REVERT: S 39 GLN cc_start: 0.7182 (pp30) cc_final: 0.6811 (tm-30) REVERT: S 60 TYR cc_start: 0.5173 (m-80) cc_final: 0.4691 (m-10) REVERT: S 65 LYS cc_start: 0.6356 (mmmt) cc_final: 0.5779 (mttt) REVERT: S 72 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7772 (pp) REVERT: I 186 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7987 (pp) REVERT: I 259 ASP cc_start: 0.8547 (p0) cc_final: 0.8306 (p0) REVERT: J 134 GLU cc_start: 0.6208 (OUTLIER) cc_final: 0.5759 (mt-10) REVERT: J 189 TRP cc_start: 0.7706 (m100) cc_final: 0.7114 (m100) REVERT: J 288 ARG cc_start: 0.2749 (mmt180) cc_final: 0.2115 (mmt90) outliers start: 101 outliers final: 53 residues processed: 440 average time/residue: 0.1948 time to fit residues: 141.4254 Evaluate side-chains 386 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 327 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 59 HIS Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 109 ARG Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 163 LYS Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain Q residue 22 CYS Chi-restraints excluded: chain Q residue 57 GLN Chi-restraints excluded: chain Q residue 68 PHE Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 182 TYR Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain R residue 121 GLN Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 169 LEU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain S residue 84 ASN Chi-restraints excluded: chain S residue 95 TYR Chi-restraints excluded: chain I residue 86 CYS Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain K residue 22 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 56 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 187 optimal weight: 0.8980 chunk 263 optimal weight: 2.9990 chunk 355 optimal weight: 2.9990 chunk 347 optimal weight: 8.9990 chunk 47 optimal weight: 8.9990 chunk 372 optimal weight: 8.9990 chunk 165 optimal weight: 0.0870 chunk 313 optimal weight: 20.0000 chunk 387 optimal weight: 10.0000 overall best weight: 2.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN L 33 HIS ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN G 229 GLN S 121 GLN ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 33 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.182055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.137075 restraints weight = 63274.674| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.90 r_work: 0.3385 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 33696 Z= 0.205 Angle : 0.608 14.592 45791 Z= 0.305 Chirality : 0.041 0.262 5048 Planarity : 0.004 0.035 5822 Dihedral : 12.542 175.048 4796 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.71 % Allowed : 13.12 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.13), residues: 4071 helix: 1.76 (0.11), residues: 2113 sheet: 1.47 (0.21), residues: 587 loop : -0.56 (0.18), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 67 TYR 0.024 0.002 TYR R 33 PHE 0.015 0.001 PHE J 160 TRP 0.034 0.002 TRP U 36 HIS 0.014 0.001 HIS U 33 Details of bonding type rmsd covalent geometry : bond 0.00481 (33668) covalent geometry : angle 0.60768 (45735) SS BOND : bond 0.00354 ( 28) SS BOND : angle 0.86423 ( 56) hydrogen bonds : bond 0.04167 ( 1887) hydrogen bonds : angle 4.22575 ( 5562) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 339 time to evaluate : 1.255 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 245 MET cc_start: 0.7693 (ppp) cc_final: 0.7370 (ppp) REVERT: L 70 ILE cc_start: 0.7544 (tp) cc_final: 0.7113 (pt) REVERT: L 80 TYR cc_start: 0.6829 (m-10) cc_final: 0.6586 (m-10) REVERT: B 47 LYS cc_start: 0.6129 (mttt) cc_final: 0.5798 (mtmt) REVERT: B 68 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.6937 (m-80) REVERT: B 74 MET cc_start: 0.7657 (mmm) cc_final: 0.7135 (mmm) REVERT: B 170 VAL cc_start: 0.7924 (OUTLIER) cc_final: 0.7609 (p) REVERT: M 82 GLN cc_start: 0.7140 (tp-100) cc_final: 0.6873 (tp40) REVERT: M 83 MET cc_start: 0.6025 (ptt) cc_final: 0.5573 (ptt) REVERT: C 171 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7282 (t0) REVERT: C 198 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7990 (mp) REVERT: O 19 ARG cc_start: 0.4985 (ttp80) cc_final: 0.4624 (ttp80) REVERT: O 60 TYR cc_start: 0.7428 (m-10) cc_final: 0.7092 (m-10) REVERT: O 110 TYR cc_start: 0.8501 (m-80) cc_final: 0.8137 (m-10) REVERT: E 91 THR cc_start: 0.0661 (OUTLIER) cc_final: 0.0269 (m) REVERT: E 109 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7405 (tmt170) REVERT: F 155 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7976 (mt-10) REVERT: F 286 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8526 (mt) REVERT: Q 57 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.6729 (tt0) REVERT: Q 80 TYR cc_start: 0.6811 (m-10) cc_final: 0.6602 (m-10) REVERT: Q 83 MET cc_start: 0.6686 (mmm) cc_final: 0.6297 (mmm) REVERT: G 137 ASP cc_start: 0.8182 (t0) cc_final: 0.7784 (t0) REVERT: G 171 ASP cc_start: 0.8178 (p0) cc_final: 0.7879 (m-30) REVERT: G 321 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8404 (pp) REVERT: R 83 MET cc_start: 0.7004 (mmp) cc_final: 0.6183 (mmp) REVERT: S 6 GLU cc_start: 0.5844 (pm20) cc_final: 0.5054 (tm-30) REVERT: S 7 SER cc_start: 0.6804 (t) cc_final: 0.6456 (m) REVERT: S 39 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.7027 (tm-30) REVERT: S 45 ARG cc_start: 0.7732 (ttm110) cc_final: 0.7454 (ttp-110) REVERT: S 60 TYR cc_start: 0.4970 (m-80) cc_final: 0.4567 (m-10) REVERT: S 65 LYS cc_start: 0.6340 (mmmt) cc_final: 0.5822 (mttt) REVERT: S 72 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8084 (pp) REVERT: I 186 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8042 (pp) REVERT: I 259 ASP cc_start: 0.8523 (p0) cc_final: 0.8239 (p0) REVERT: I 262 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7655 (mp0) REVERT: J 134 GLU cc_start: 0.6274 (OUTLIER) cc_final: 0.5524 (mt-10) REVERT: J 189 TRP cc_start: 0.7710 (m100) cc_final: 0.7112 (m100) REVERT: J 220 TRP cc_start: 0.6497 (t-100) cc_final: 0.6063 (t-100) REVERT: J 288 ARG cc_start: 0.2632 (mmt180) cc_final: 0.1878 (mmt90) REVERT: K 192 LEU cc_start: 0.7135 (pp) cc_final: 0.6429 (mt) REVERT: U 11 LEU cc_start: 0.2598 (OUTLIER) cc_final: 0.2117 (mp) outliers start: 127 outliers final: 70 residues processed: 437 average time/residue: 0.2103 time to fit residues: 150.3794 Evaluate side-chains 399 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 315 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 59 HIS Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 109 ARG Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 163 LYS Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain Q residue 22 CYS Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 57 GLN Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 182 TYR Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 169 LEU Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain S residue 84 ASN Chi-restraints excluded: chain S residue 95 TYR Chi-restraints excluded: chain I residue 86 CYS Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 260 ASP Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain U residue 11 LEU Chi-restraints excluded: chain U residue 93 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 316 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 369 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 295 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 197 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 379 optimal weight: 8.9990 chunk 62 optimal weight: 0.0970 chunk 243 optimal weight: 0.0980 overall best weight: 1.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN B 226 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 13 GLN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 33 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.182825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.136972 restraints weight = 63619.189| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 3.05 r_work: 0.3399 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33696 Z= 0.149 Angle : 0.580 13.505 45791 Z= 0.287 Chirality : 0.039 0.251 5048 Planarity : 0.004 0.063 5822 Dihedral : 12.279 175.531 4796 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.27 % Allowed : 13.70 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.13), residues: 4071 helix: 1.88 (0.11), residues: 2112 sheet: 1.47 (0.21), residues: 587 loop : -0.53 (0.18), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 38 TYR 0.026 0.001 TYR K 220 PHE 0.027 0.001 PHE J 160 TRP 0.032 0.001 TRP U 36 HIS 0.010 0.001 HIS U 33 Details of bonding type rmsd covalent geometry : bond 0.00340 (33668) covalent geometry : angle 0.57967 (45735) SS BOND : bond 0.00298 ( 28) SS BOND : angle 0.74368 ( 56) hydrogen bonds : bond 0.03822 ( 1887) hydrogen bonds : angle 4.08482 ( 5562) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 345 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 70 ILE cc_start: 0.7684 (tp) cc_final: 0.7217 (pt) REVERT: B 47 LYS cc_start: 0.6175 (mttt) cc_final: 0.5885 (mtmt) REVERT: B 68 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.6950 (m-80) REVERT: B 74 MET cc_start: 0.7675 (mmm) cc_final: 0.7139 (mmm) REVERT: B 170 VAL cc_start: 0.7821 (OUTLIER) cc_final: 0.7455 (p) REVERT: M 20 LEU cc_start: 0.7080 (mp) cc_final: 0.6627 (mt) REVERT: M 82 GLN cc_start: 0.7120 (tp-100) cc_final: 0.6871 (tp40) REVERT: C 171 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7114 (t0) REVERT: O 19 ARG cc_start: 0.4968 (ttp80) cc_final: 0.4734 (ttp80) REVERT: O 60 TYR cc_start: 0.7371 (m-10) cc_final: 0.7058 (m-10) REVERT: E 91 THR cc_start: 0.0600 (OUTLIER) cc_final: 0.0215 (m) REVERT: E 109 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7389 (tmt170) REVERT: F 155 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7967 (mt-10) REVERT: F 285 TYR cc_start: 0.8589 (t80) cc_final: 0.8384 (t80) REVERT: F 286 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8533 (mt) REVERT: Q 4 LEU cc_start: 0.7381 (mm) cc_final: 0.6995 (mt) REVERT: Q 57 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.6707 (tt0) REVERT: Q 80 TYR cc_start: 0.6774 (m-10) cc_final: 0.6563 (m-10) REVERT: G 137 ASP cc_start: 0.8228 (t0) cc_final: 0.7807 (t0) REVERT: G 171 ASP cc_start: 0.7947 (p0) cc_final: 0.7693 (m-30) REVERT: G 321 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8377 (pp) REVERT: R 82 GLN cc_start: 0.7551 (mt0) cc_final: 0.7049 (mp10) REVERT: R 83 MET cc_start: 0.6939 (mmp) cc_final: 0.5786 (mmt) REVERT: H 205 LEU cc_start: 0.8851 (tt) cc_final: 0.8633 (tp) REVERT: S 39 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.7233 (tm-30) REVERT: S 45 ARG cc_start: 0.7747 (ttm110) cc_final: 0.7217 (ttp-110) REVERT: S 60 TYR cc_start: 0.5204 (m-80) cc_final: 0.4500 (m-10) REVERT: S 65 LYS cc_start: 0.6185 (mmmt) cc_final: 0.5842 (mmtt) REVERT: I 87 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.7136 (tt0) REVERT: I 186 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.8019 (pp) REVERT: I 259 ASP cc_start: 0.8475 (p0) cc_final: 0.8227 (p0) REVERT: I 262 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7438 (mp0) REVERT: J 134 GLU cc_start: 0.6087 (OUTLIER) cc_final: 0.5290 (mt-10) REVERT: J 189 TRP cc_start: 0.7703 (m100) cc_final: 0.7092 (m100) REVERT: J 288 ARG cc_start: 0.2611 (mmt180) cc_final: 0.1875 (mmt90) REVERT: K 192 LEU cc_start: 0.7462 (pp) cc_final: 0.6802 (mt) REVERT: U 11 LEU cc_start: 0.2583 (OUTLIER) cc_final: 0.2111 (mp) REVERT: N 36 TRP cc_start: 0.3500 (m100) cc_final: 0.2800 (m100) outliers start: 112 outliers final: 73 residues processed: 429 average time/residue: 0.2121 time to fit residues: 150.2857 Evaluate side-chains 399 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 313 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 59 HIS Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 109 ARG Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain Q residue 22 CYS Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 57 GLN Chi-restraints excluded: chain Q residue 68 PHE Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 169 LEU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 84 ASN Chi-restraints excluded: chain S residue 95 TYR Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 260 ASP Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 113 ILE Chi-restraints excluded: chain K residue 218 HIS Chi-restraints excluded: chain U residue 11 LEU Chi-restraints excluded: chain U residue 93 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 91 optimal weight: 8.9990 chunk 273 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 401 optimal weight: 30.0000 chunk 48 optimal weight: 0.0170 chunk 108 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 183 optimal weight: 0.5980 chunk 392 optimal weight: 8.9990 chunk 313 optimal weight: 6.9990 chunk 169 optimal weight: 0.6980 overall best weight: 1.0220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 111 HIS Q 121 GLN H 300 HIS H 304 GLN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 33 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.183538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.136343 restraints weight = 63665.397| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.95 r_work: 0.3413 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33696 Z= 0.121 Angle : 0.566 13.671 45791 Z= 0.279 Chirality : 0.039 0.283 5048 Planarity : 0.003 0.033 5822 Dihedral : 11.794 177.402 4794 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.75 % Allowed : 14.81 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.14), residues: 4071 helix: 1.98 (0.11), residues: 2131 sheet: 1.38 (0.20), residues: 622 loop : -0.58 (0.18), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 124 TYR 0.020 0.001 TYR K 220 PHE 0.016 0.001 PHE J 160 TRP 0.033 0.001 TRP U 36 HIS 0.009 0.001 HIS U 33 Details of bonding type rmsd covalent geometry : bond 0.00268 (33668) covalent geometry : angle 0.56572 (45735) SS BOND : bond 0.00267 ( 28) SS BOND : angle 1.01092 ( 56) hydrogen bonds : bond 0.03545 ( 1887) hydrogen bonds : angle 3.93622 ( 5562) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 341 time to evaluate : 1.127 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: L 36 TRP cc_start: 0.6189 (m100) cc_final: 0.5583 (m100) REVERT: L 70 ILE cc_start: 0.7714 (tp) cc_final: 0.7291 (pt) REVERT: B 47 LYS cc_start: 0.6183 (mttt) cc_final: 0.5880 (mtmt) REVERT: M 82 GLN cc_start: 0.7159 (tp-100) cc_final: 0.6879 (tp40) REVERT: C 171 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7039 (t0) REVERT: O 60 TYR cc_start: 0.7355 (m-10) cc_final: 0.7024 (m-10) REVERT: O 78 THR cc_start: 0.6017 (OUTLIER) cc_final: 0.4517 (t) REVERT: O 80 TYR cc_start: 0.7568 (m-10) cc_final: 0.7320 (m-80) REVERT: E 91 THR cc_start: 0.0777 (OUTLIER) cc_final: 0.0469 (m) REVERT: E 109 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7470 (tmt170) REVERT: F 155 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8220 (mt-10) REVERT: F 298 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.7267 (ptp-170) REVERT: Q 57 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.6826 (tt0) REVERT: G 128 TYR cc_start: 0.8761 (t80) cc_final: 0.8442 (t80) REVERT: G 137 ASP cc_start: 0.8320 (t0) cc_final: 0.7860 (t0) REVERT: G 171 ASP cc_start: 0.8058 (p0) cc_final: 0.7798 (m-30) REVERT: G 321 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8434 (pp) REVERT: R 80 TYR cc_start: 0.7448 (m-10) cc_final: 0.7151 (m-10) REVERT: H 205 LEU cc_start: 0.8916 (tt) cc_final: 0.8697 (tp) REVERT: S 39 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7385 (tm-30) REVERT: S 45 ARG cc_start: 0.7714 (ttm110) cc_final: 0.7280 (ttp-110) REVERT: S 60 TYR cc_start: 0.4997 (m-80) cc_final: 0.4094 (m-10) REVERT: S 65 LYS cc_start: 0.6355 (mmmt) cc_final: 0.6083 (mmtt) REVERT: I 186 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7947 (pp) REVERT: I 262 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7545 (mp0) REVERT: J 134 GLU cc_start: 0.6215 (OUTLIER) cc_final: 0.5372 (mt-10) REVERT: J 189 TRP cc_start: 0.7716 (m100) cc_final: 0.7150 (m100) REVERT: J 198 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8012 (mm) REVERT: J 220 TRP cc_start: 0.6314 (t-100) cc_final: 0.5554 (m-90) REVERT: J 288 ARG cc_start: 0.2600 (mmt180) cc_final: 0.1853 (mmt90) REVERT: K 192 LEU cc_start: 0.7783 (pp) cc_final: 0.7214 (mp) REVERT: U 11 LEU cc_start: 0.2506 (OUTLIER) cc_final: 0.2287 (mp) REVERT: N 36 TRP cc_start: 0.3934 (m100) cc_final: 0.3138 (m100) REVERT: N 95 TYR cc_start: 0.6016 (m-80) cc_final: 0.5800 (m-80) outliers start: 94 outliers final: 61 residues processed: 415 average time/residue: 0.1896 time to fit residues: 128.9506 Evaluate side-chains 382 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 309 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 59 HIS Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 109 ARG Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain Q residue 22 CYS Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 57 GLN Chi-restraints excluded: chain Q residue 68 PHE Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain H residue 169 LEU Chi-restraints excluded: chain H residue 262 GLU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 84 ASN Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 260 ASP Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 113 ILE Chi-restraints excluded: chain K residue 248 ILE Chi-restraints excluded: chain U residue 11 LEU Chi-restraints excluded: chain U residue 93 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 65 optimal weight: 40.0000 chunk 234 optimal weight: 2.9990 chunk 338 optimal weight: 9.9990 chunk 353 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 172 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 236 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN ** C 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 13 GLN R 82 GLN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 33 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.181453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.136103 restraints weight = 63785.044| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 3.01 r_work: 0.3371 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 33696 Z= 0.216 Angle : 0.625 14.893 45791 Z= 0.310 Chirality : 0.042 0.240 5048 Planarity : 0.004 0.044 5822 Dihedral : 11.669 177.580 4792 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.27 % Allowed : 14.78 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.13), residues: 4071 helix: 1.81 (0.11), residues: 2136 sheet: 1.35 (0.20), residues: 592 loop : -0.65 (0.18), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 67 TYR 0.023 0.002 TYR D 285 PHE 0.021 0.002 PHE A 18 TRP 0.035 0.002 TRP U 36 HIS 0.012 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00508 (33668) covalent geometry : angle 0.62432 (45735) SS BOND : bond 0.00431 ( 28) SS BOND : angle 1.05414 ( 56) hydrogen bonds : bond 0.03927 ( 1887) hydrogen bonds : angle 4.05020 ( 5562) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 321 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.8584 (mmm) cc_final: 0.8328 (mmm) REVERT: A 244 MET cc_start: 0.6365 (mmm) cc_final: 0.6075 (mmm) REVERT: L 70 ILE cc_start: 0.7697 (tp) cc_final: 0.7303 (pt) REVERT: B 47 LYS cc_start: 0.6491 (mttt) cc_final: 0.6137 (mtmt) REVERT: B 68 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.6975 (m-80) REVERT: B 74 MET cc_start: 0.7673 (mmm) cc_final: 0.7109 (mmm) REVERT: M 20 LEU cc_start: 0.6159 (tt) cc_final: 0.5614 (mm) REVERT: M 83 MET cc_start: 0.5846 (mpp) cc_final: 0.5412 (ptp) REVERT: D 285 TYR cc_start: 0.8222 (t80) cc_final: 0.8008 (t80) REVERT: O 19 ARG cc_start: 0.4840 (ttp80) cc_final: 0.4533 (ttp80) REVERT: O 38 ARG cc_start: 0.7263 (ptm160) cc_final: 0.6860 (ptm-80) REVERT: O 60 TYR cc_start: 0.7331 (m-10) cc_final: 0.7063 (m-10) REVERT: O 80 TYR cc_start: 0.7539 (m-10) cc_final: 0.7181 (m-80) REVERT: E 91 THR cc_start: 0.0408 (OUTLIER) cc_final: 0.0092 (m) REVERT: E 109 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7889 (mtp180) REVERT: F 155 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7980 (mt-10) REVERT: F 286 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8538 (mt) REVERT: Q 57 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.6771 (tt0) REVERT: G 137 ASP cc_start: 0.8274 (t0) cc_final: 0.7838 (t0) REVERT: G 171 ASP cc_start: 0.7913 (p0) cc_final: 0.7559 (m-30) REVERT: G 172 PHE cc_start: 0.7697 (m-80) cc_final: 0.7008 (t80) REVERT: G 321 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8458 (pp) REVERT: R 80 TYR cc_start: 0.7470 (m-10) cc_final: 0.7106 (m-10) REVERT: R 83 MET cc_start: 0.6937 (mmp) cc_final: 0.5785 (mmt) REVERT: H 100 PHE cc_start: 0.8193 (m-80) cc_final: 0.7957 (m-80) REVERT: S 39 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7400 (tm-30) REVERT: S 45 ARG cc_start: 0.7830 (ttm110) cc_final: 0.7473 (ttp-110) REVERT: S 60 TYR cc_start: 0.5025 (m-80) cc_final: 0.4070 (m-10) REVERT: S 65 LYS cc_start: 0.6271 (mmmt) cc_final: 0.6066 (mmtt) REVERT: I 186 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7989 (pp) REVERT: I 262 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7582 (mp0) REVERT: J 134 GLU cc_start: 0.6236 (OUTLIER) cc_final: 0.5402 (mt-10) REVERT: J 189 TRP cc_start: 0.7659 (m100) cc_final: 0.7086 (m100) REVERT: J 198 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8013 (mm) REVERT: J 220 TRP cc_start: 0.6353 (t-100) cc_final: 0.5699 (m-90) REVERT: J 288 ARG cc_start: 0.2666 (mmt180) cc_final: 0.1909 (mmt90) REVERT: K 192 LEU cc_start: 0.7766 (pp) cc_final: 0.7134 (mt) REVERT: U 11 LEU cc_start: 0.2497 (OUTLIER) cc_final: 0.2172 (mp) REVERT: N 38 ARG cc_start: 0.5917 (OUTLIER) cc_final: 0.4854 (mtp-110) outliers start: 112 outliers final: 82 residues processed: 414 average time/residue: 0.2131 time to fit residues: 145.0712 Evaluate side-chains 393 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 299 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 59 HIS Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 109 ARG Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain Q residue 22 CYS Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 57 GLN Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 182 TYR Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 82 GLN Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain H residue 53 ASN Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 169 LEU Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 262 GLU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 84 ASN Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 260 ASP Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain U residue 11 LEU Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 72 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 244 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 198 optimal weight: 0.7980 chunk 393 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 392 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 302 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 13 GLN R 77 ASN ** R 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 HIS N 121 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.181690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.136603 restraints weight = 63512.886| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.96 r_work: 0.3380 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 33696 Z= 0.189 Angle : 0.608 14.441 45791 Z= 0.301 Chirality : 0.041 0.212 5048 Planarity : 0.004 0.044 5822 Dihedral : 11.345 177.889 4792 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.16 % Allowed : 15.07 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.13), residues: 4071 helix: 1.81 (0.11), residues: 2136 sheet: 1.31 (0.20), residues: 592 loop : -0.69 (0.18), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Q 67 TYR 0.021 0.001 TYR E 287 PHE 0.031 0.001 PHE Q 68 TRP 0.035 0.002 TRP U 36 HIS 0.010 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00444 (33668) covalent geometry : angle 0.60743 (45735) SS BOND : bond 0.00348 ( 28) SS BOND : angle 0.93605 ( 56) hydrogen bonds : bond 0.03786 ( 1887) hydrogen bonds : angle 4.00336 ( 5562) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 311 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.6459 (mmm) cc_final: 0.6245 (mmm) REVERT: L 36 TRP cc_start: 0.5845 (m100) cc_final: 0.5426 (m100) REVERT: L 70 ILE cc_start: 0.7725 (tp) cc_final: 0.7318 (pt) REVERT: B 47 LYS cc_start: 0.6675 (mttt) cc_final: 0.6256 (mtmt) REVERT: B 68 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.6979 (m-80) REVERT: B 74 MET cc_start: 0.7667 (mmm) cc_final: 0.7089 (mmm) REVERT: M 20 LEU cc_start: 0.5757 (tt) cc_final: 0.5184 (mm) REVERT: C 75 LEU cc_start: 0.8888 (mp) cc_final: 0.8361 (tt) REVERT: C 285 TYR cc_start: 0.5232 (p90) cc_final: 0.4993 (p90) REVERT: D 285 TYR cc_start: 0.8188 (t80) cc_final: 0.7985 (t80) REVERT: O 19 ARG cc_start: 0.4796 (ttp80) cc_final: 0.4315 (ttp80) REVERT: O 38 ARG cc_start: 0.7262 (ptm160) cc_final: 0.6858 (ptm-80) REVERT: O 39 GLN cc_start: 0.6303 (pt0) cc_final: 0.5302 (pp30) REVERT: O 60 TYR cc_start: 0.7372 (m-10) cc_final: 0.7088 (m-10) REVERT: E 91 THR cc_start: 0.0184 (OUTLIER) cc_final: -0.0021 (m) REVERT: E 109 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7837 (mtp180) REVERT: F 155 GLU cc_start: 0.8207 (mm-30) cc_final: 0.8001 (mt-10) REVERT: F 286 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8567 (mt) REVERT: Q 57 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.6752 (tt0) REVERT: Q 83 MET cc_start: 0.5645 (mmm) cc_final: 0.5214 (mmm) REVERT: G 137 ASP cc_start: 0.8269 (t0) cc_final: 0.7828 (t0) REVERT: G 171 ASP cc_start: 0.7925 (p0) cc_final: 0.7549 (m-30) REVERT: G 172 PHE cc_start: 0.7875 (m-80) cc_final: 0.7284 (t80) REVERT: G 321 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8432 (pp) REVERT: R 80 TYR cc_start: 0.7477 (m-10) cc_final: 0.7242 (m-80) REVERT: R 83 MET cc_start: 0.6896 (mmp) cc_final: 0.5778 (mmt) REVERT: H 100 PHE cc_start: 0.8216 (m-80) cc_final: 0.7974 (m-80) REVERT: S 39 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7416 (tm-30) REVERT: S 45 ARG cc_start: 0.7794 (ttm110) cc_final: 0.7441 (ttp-110) REVERT: S 60 TYR cc_start: 0.5058 (m-80) cc_final: 0.4028 (m-10) REVERT: I 186 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.8015 (pp) REVERT: I 262 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7468 (mp0) REVERT: J 134 GLU cc_start: 0.6231 (OUTLIER) cc_final: 0.5366 (mt-10) REVERT: J 189 TRP cc_start: 0.7649 (m100) cc_final: 0.7109 (m100) REVERT: J 198 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8083 (mm) REVERT: J 220 TRP cc_start: 0.6289 (t-100) cc_final: 0.5590 (m-90) REVERT: J 288 ARG cc_start: 0.2678 (mmt180) cc_final: 0.1908 (mmt90) REVERT: K 192 LEU cc_start: 0.7766 (pp) cc_final: 0.7152 (mp) REVERT: U 11 LEU cc_start: 0.2558 (OUTLIER) cc_final: 0.2315 (mp) REVERT: N 36 TRP cc_start: 0.3754 (m100) cc_final: 0.2631 (m100) REVERT: N 38 ARG cc_start: 0.5895 (OUTLIER) cc_final: 0.4907 (mtp-110) REVERT: N 95 TYR cc_start: 0.5719 (m-80) cc_final: 0.5451 (m-80) outliers start: 108 outliers final: 83 residues processed: 400 average time/residue: 0.2043 time to fit residues: 134.9599 Evaluate side-chains 391 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 296 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 59 HIS Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 109 ARG Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain Q residue 22 CYS Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 57 GLN Chi-restraints excluded: chain Q residue 68 PHE Chi-restraints excluded: chain Q residue 70 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain R residue 77 ASN Chi-restraints excluded: chain R residue 107 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 169 LEU Chi-restraints excluded: chain H residue 262 GLU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 84 ASN Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 260 ASP Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain U residue 11 LEU Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 72 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 165 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 274 optimal weight: 3.9990 chunk 179 optimal weight: 0.4980 chunk 154 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 241 optimal weight: 0.7980 chunk 321 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 121 GLN P 13 GLN R 77 ASN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.183308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.138561 restraints weight = 63385.423| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.74 r_work: 0.3431 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33696 Z= 0.116 Angle : 0.574 12.434 45791 Z= 0.281 Chirality : 0.039 0.233 5048 Planarity : 0.003 0.067 5822 Dihedral : 10.922 179.624 4792 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.72 % Allowed : 15.43 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.13), residues: 4071 helix: 2.01 (0.11), residues: 2138 sheet: 1.54 (0.21), residues: 522 loop : -0.67 (0.17), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG Q 67 TYR 0.029 0.001 TYR K 220 PHE 0.026 0.001 PHE Q 68 TRP 0.036 0.001 TRP U 36 HIS 0.006 0.001 HIS K 246 Details of bonding type rmsd covalent geometry : bond 0.00251 (33668) covalent geometry : angle 0.57305 (45735) SS BOND : bond 0.00242 ( 28) SS BOND : angle 0.86568 ( 56) hydrogen bonds : bond 0.03390 ( 1887) hydrogen bonds : angle 3.86730 ( 5562) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 319 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ILE cc_start: 0.6891 (mt) cc_final: 0.6611 (tt) REVERT: L 36 TRP cc_start: 0.5957 (m100) cc_final: 0.5687 (m100) REVERT: L 70 ILE cc_start: 0.7955 (tp) cc_final: 0.7417 (pt) REVERT: B 47 LYS cc_start: 0.6612 (mttt) cc_final: 0.6214 (mtmt) REVERT: B 68 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.6959 (m-80) REVERT: B 74 MET cc_start: 0.7644 (mmm) cc_final: 0.7112 (mmm) REVERT: M 20 LEU cc_start: 0.5929 (tt) cc_final: 0.5443 (mm) REVERT: C 75 LEU cc_start: 0.8865 (mp) cc_final: 0.8332 (tt) REVERT: C 171 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.6835 (t0) REVERT: D 285 TYR cc_start: 0.8029 (t80) cc_final: 0.7810 (t80) REVERT: O 29 ARG cc_start: 0.7601 (mtp-110) cc_final: 0.7171 (tpm170) REVERT: O 38 ARG cc_start: 0.7095 (ptm160) cc_final: 0.6612 (ptm-80) REVERT: O 39 GLN cc_start: 0.6287 (pt0) cc_final: 0.5368 (pp30) REVERT: O 60 TYR cc_start: 0.7213 (m-10) cc_final: 0.6916 (m-10) REVERT: E 91 THR cc_start: -0.0199 (OUTLIER) cc_final: -0.0509 (m) REVERT: E 109 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7320 (tmt170) REVERT: F 155 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7924 (mt-10) REVERT: F 286 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8568 (mt) REVERT: Q 57 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.6733 (tt0) REVERT: G 128 TYR cc_start: 0.8666 (t80) cc_final: 0.8339 (t80) REVERT: G 137 ASP cc_start: 0.8234 (t0) cc_final: 0.7850 (t0) REVERT: G 171 ASP cc_start: 0.7821 (p0) cc_final: 0.7593 (m-30) REVERT: G 321 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8383 (pp) REVERT: R 80 TYR cc_start: 0.7441 (m-10) cc_final: 0.7071 (m-10) REVERT: R 83 MET cc_start: 0.6827 (mmp) cc_final: 0.5769 (mmt) REVERT: R 89 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6648 (pp20) REVERT: H 100 PHE cc_start: 0.8166 (m-80) cc_final: 0.7916 (m-80) REVERT: S 45 ARG cc_start: 0.7750 (ttm110) cc_final: 0.7440 (ttp-110) REVERT: S 60 TYR cc_start: 0.4546 (m-80) cc_final: 0.4259 (m-10) REVERT: S 65 LYS cc_start: 0.5444 (mmtt) cc_final: 0.4936 (mttt) REVERT: I 186 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7926 (pp) REVERT: I 262 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7451 (mp0) REVERT: J 134 GLU cc_start: 0.6162 (OUTLIER) cc_final: 0.5295 (mt-10) REVERT: J 189 TRP cc_start: 0.7614 (m100) cc_final: 0.7081 (m100) REVERT: J 198 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8111 (mm) REVERT: J 220 TRP cc_start: 0.6155 (t-100) cc_final: 0.5508 (m-90) REVERT: J 288 ARG cc_start: 0.2661 (mmt180) cc_final: 0.1921 (mmt90) REVERT: K 192 LEU cc_start: 0.7679 (pp) cc_final: 0.7077 (mp) REVERT: U 11 LEU cc_start: 0.2552 (OUTLIER) cc_final: 0.2313 (mp) REVERT: N 36 TRP cc_start: 0.3983 (m100) cc_final: 0.2783 (m100) REVERT: N 38 ARG cc_start: 0.6249 (OUTLIER) cc_final: 0.5267 (mtp-110) REVERT: N 95 TYR cc_start: 0.5716 (m-80) cc_final: 0.5416 (m-80) outliers start: 93 outliers final: 70 residues processed: 395 average time/residue: 0.2043 time to fit residues: 131.9446 Evaluate side-chains 382 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 300 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 59 HIS Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 109 ARG Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain Q residue 22 CYS Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 57 GLN Chi-restraints excluded: chain Q residue 68 PHE Chi-restraints excluded: chain Q residue 70 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain R residue 44 GLU Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 169 LEU Chi-restraints excluded: chain H residue 262 GLU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 84 ASN Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 260 ASP Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain U residue 11 LEU Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 72 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 218 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 61 optimal weight: 30.0000 chunk 225 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 41 optimal weight: 20.0000 chunk 178 optimal weight: 0.7980 chunk 329 optimal weight: 30.0000 chunk 192 optimal weight: 4.9990 chunk 176 optimal weight: 20.0000 chunk 185 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 13 GLN R 77 ASN ** R 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 238 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.182379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.137302 restraints weight = 63929.499| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.97 r_work: 0.3409 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33696 Z= 0.155 Angle : 0.596 13.323 45791 Z= 0.294 Chirality : 0.040 0.205 5048 Planarity : 0.004 0.056 5822 Dihedral : 10.671 179.791 4792 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.72 % Allowed : 15.75 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.13), residues: 4071 helix: 1.95 (0.11), residues: 2144 sheet: 1.58 (0.21), residues: 508 loop : -0.66 (0.17), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Q 67 TYR 0.032 0.001 TYR K 220 PHE 0.026 0.001 PHE Q 68 TRP 0.050 0.002 TRP U 36 HIS 0.008 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00359 (33668) covalent geometry : angle 0.59574 (45735) SS BOND : bond 0.00299 ( 28) SS BOND : angle 0.84385 ( 56) hydrogen bonds : bond 0.03554 ( 1887) hydrogen bonds : angle 3.88444 ( 5562) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 308 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 36 TRP cc_start: 0.5763 (m100) cc_final: 0.5505 (m100) REVERT: B 47 LYS cc_start: 0.6599 (mttt) cc_final: 0.6249 (mtmt) REVERT: B 68 PHE cc_start: 0.7887 (OUTLIER) cc_final: 0.6970 (m-80) REVERT: B 74 MET cc_start: 0.7656 (mmm) cc_final: 0.7130 (mmm) REVERT: M 20 LEU cc_start: 0.5731 (tt) cc_final: 0.5281 (mm) REVERT: C 75 LEU cc_start: 0.8885 (mp) cc_final: 0.8355 (tt) REVERT: C 171 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.6866 (t0) REVERT: O 29 ARG cc_start: 0.7584 (mtp-110) cc_final: 0.7172 (tpm170) REVERT: O 38 ARG cc_start: 0.6907 (ptm160) cc_final: 0.6549 (ptm-80) REVERT: O 39 GLN cc_start: 0.6305 (pt0) cc_final: 0.5312 (pp30) REVERT: O 60 TYR cc_start: 0.7224 (m-10) cc_final: 0.6903 (m-10) REVERT: O 72 LEU cc_start: 0.7048 (tp) cc_final: 0.6839 (pt) REVERT: E 91 THR cc_start: -0.0339 (OUTLIER) cc_final: -0.0556 (m) REVERT: E 109 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7382 (tmt170) REVERT: F 155 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7959 (mt-10) REVERT: Q 4 LEU cc_start: 0.6884 (mm) cc_final: 0.6456 (tp) REVERT: Q 57 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.6880 (tt0) REVERT: G 137 ASP cc_start: 0.8248 (t0) cc_final: 0.7827 (t0) REVERT: G 171 ASP cc_start: 0.7811 (p0) cc_final: 0.7522 (m-30) REVERT: G 172 PHE cc_start: 0.7681 (m-80) cc_final: 0.7067 (t80) REVERT: G 321 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8411 (pp) REVERT: R 83 MET cc_start: 0.6861 (mmp) cc_final: 0.5769 (mmt) REVERT: R 89 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6650 (pp20) REVERT: H 100 PHE cc_start: 0.8145 (m-80) cc_final: 0.7923 (m-80) REVERT: S 45 ARG cc_start: 0.7794 (ttm110) cc_final: 0.7410 (ttp-110) REVERT: I 262 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7528 (mp0) REVERT: J 134 GLU cc_start: 0.6190 (OUTLIER) cc_final: 0.5290 (mt-10) REVERT: J 189 TRP cc_start: 0.7621 (m100) cc_final: 0.7097 (m100) REVERT: J 198 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8050 (mm) REVERT: J 220 TRP cc_start: 0.6150 (t-100) cc_final: 0.5595 (m-90) REVERT: J 288 ARG cc_start: 0.2703 (mmt180) cc_final: 0.1941 (mmt90) REVERT: K 192 LEU cc_start: 0.7619 (pp) cc_final: 0.7031 (mp) REVERT: U 11 LEU cc_start: 0.2568 (OUTLIER) cc_final: 0.2322 (mp) REVERT: N 36 TRP cc_start: 0.4183 (m100) cc_final: 0.3918 (m100) REVERT: N 38 ARG cc_start: 0.6245 (OUTLIER) cc_final: 0.5210 (mtp-110) outliers start: 93 outliers final: 78 residues processed: 386 average time/residue: 0.1967 time to fit residues: 124.3637 Evaluate side-chains 386 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 298 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 59 HIS Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 109 ARG Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain Q residue 22 CYS Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 57 GLN Chi-restraints excluded: chain Q residue 68 PHE Chi-restraints excluded: chain Q residue 70 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain R residue 44 GLU Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 169 LEU Chi-restraints excluded: chain H residue 262 GLU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 84 ASN Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 260 ASP Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain U residue 11 LEU Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 72 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 138 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 350 optimal weight: 9.9990 chunk 335 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 42 optimal weight: 20.0000 chunk 233 optimal weight: 0.5980 chunk 174 optimal weight: 0.9980 chunk 121 optimal weight: 6.9990 chunk 266 optimal weight: 0.7980 chunk 314 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN P 13 GLN Q 121 GLN R 77 ASN ** R 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.183562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.139359 restraints weight = 63954.397| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 2.89 r_work: 0.3442 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33696 Z= 0.115 Angle : 0.582 11.948 45791 Z= 0.285 Chirality : 0.039 0.188 5048 Planarity : 0.003 0.060 5822 Dihedral : 10.158 179.645 4792 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.45 % Allowed : 16.18 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.14), residues: 4071 helix: 2.07 (0.11), residues: 2144 sheet: 1.57 (0.21), residues: 508 loop : -0.62 (0.17), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Q 67 TYR 0.028 0.001 TYR K 220 PHE 0.043 0.001 PHE J 69 TRP 0.044 0.001 TRP U 36 HIS 0.007 0.001 HIS J 300 Details of bonding type rmsd covalent geometry : bond 0.00254 (33668) covalent geometry : angle 0.58176 (45735) SS BOND : bond 0.00246 ( 28) SS BOND : angle 0.77000 ( 56) hydrogen bonds : bond 0.03317 ( 1887) hydrogen bonds : angle 3.80477 ( 5562) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9440.20 seconds wall clock time: 162 minutes 7.73 seconds (9727.73 seconds total)