Starting phenix.real_space_refine on Wed Nov 19 07:15:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6b47_7051/11_2025/6b47_7051.cif Found real_map, /net/cci-nas-00/data/ceres_data/6b47_7051/11_2025/6b47_7051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6b47_7051/11_2025/6b47_7051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6b47_7051/11_2025/6b47_7051.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6b47_7051/11_2025/6b47_7051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6b47_7051/11_2025/6b47_7051.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.001 sd= 0.010 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 59 5.49 5 S 20 5.16 5 C 13479 2.51 5 N 4171 2.21 5 O 4484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22213 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 2079 Classifications: {'peptide': 424} Incomplete info: {'backbone_only': 310} Link IDs: {'PTRANS': 24, 'TRANS': 399} Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1373 Unresolved non-hydrogen angles: 1987 Unresolved non-hydrogen dihedrals: 884 Unresolved non-hydrogen chiralities: 392 Planarities with less than four sites: {'GLN:plan1': 29, 'GLU:plan': 24, 'ARG:plan': 29, 'PHE:plan': 11, 'ASP:plan': 20, 'HIS:plan': 9, 'TRP:plan': 9, 'ASN:plan1': 13, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 726 Chain: "B" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2374 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 23, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2272 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Chain: "D" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2554 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2561 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2561 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2557 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2557 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "K" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 668 Classifications: {'peptide': 87} Link IDs: {'TRANS': 86} Chain: "L" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 758 Classifications: {'peptide': 189} Incomplete info: {'backbone_only': 173, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 173} Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 806 Unresolved non-hydrogen angles: 1152 Unresolved non-hydrogen dihedrals: 534 Unresolved non-hydrogen chiralities: 219 Planarities with less than four sites: {'ASP:plan': 12, 'HIS:plan': 8, 'TYR:plan': 3, 'ARG:plan': 24, 'GLU:plan': 11, 'PHE:plan': 10, 'GLN:plan1': 9, 'TRP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 414 Chain: "M" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1272 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 11, 'rna3p_pur': 20, 'rna3p_pyr': 19} Link IDs: {'rna2p': 19, 'rna3p': 40} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 5.72, per 1000 atoms: 0.26 Number of scatterers: 22213 At special positions: 0 Unit cell: (152.281, 122.254, 153.353, 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 20 16.00 P 59 15.00 O 4484 8.00 N 4171 7.00 C 13479 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.89 Conformation dependent library (CDL) restraints added in 1.2 seconds 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4550 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 47 sheets defined 32.3% alpha, 19.5% beta 1 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'A' and resid 14 through 29 removed outlier: 3.737A pdb=" N LYS A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.975A pdb=" N HIS A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 59 removed outlier: 4.242A pdb=" N ARG A 59 " --> pdb=" O ASP A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.559A pdb=" N GLU A 99 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 100 " --> pdb=" O SER A 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 96 through 100' Processing helix chain 'A' and resid 114 through 122 removed outlier: 3.805A pdb=" N PHE A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 148 through 161 Processing helix chain 'A' and resid 195 through 211 Processing helix chain 'A' and resid 213 through 223 Processing helix chain 'A' and resid 294 through 307 Processing helix chain 'A' and resid 317 through 341 removed outlier: 3.523A pdb=" N ARG A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN A 324 " --> pdb=" O GLN A 320 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS A 330 " --> pdb=" O VAL A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 372 through 382 Processing helix chain 'A' and resid 384 through 397 Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.928A pdb=" N LEU A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 434 removed outlier: 3.869A pdb=" N ASP A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 48 removed outlier: 3.951A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 119 removed outlier: 3.685A pdb=" N LEU B 118 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP B 119 " --> pdb=" O ASP B 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 115 through 119' Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 165 through 177 Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 189 through 201 Processing helix chain 'B' and resid 206 through 212 removed outlier: 3.638A pdb=" N LEU B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 39 removed outlier: 3.839A pdb=" N GLU C 38 " --> pdb=" O ALA C 35 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TRP C 39 " --> pdb=" O SER C 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 35 through 39' Processing helix chain 'C' and resid 111 through 129 Processing helix chain 'C' and resid 131 through 144 Processing helix chain 'C' and resid 189 through 205 Processing helix chain 'C' and resid 256 through 265 removed outlier: 3.671A pdb=" N ILE C 260 " --> pdb=" O HIS C 256 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG C 265 " --> pdb=" O GLY C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 313 Processing helix chain 'C' and resid 319 through 333 Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.502A pdb=" N GLN D 72 " --> pdb=" O ASP D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 129 removed outlier: 3.514A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 144 Processing helix chain 'D' and resid 189 through 204 Processing helix chain 'D' and resid 256 through 265 removed outlier: 3.582A pdb=" N ILE D 260 " --> pdb=" O HIS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 314 removed outlier: 3.624A pdb=" N ARG D 314 " --> pdb=" O ASN D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 333 Processing helix chain 'E' and resid 32 through 39 removed outlier: 3.682A pdb=" N SER E 36 " --> pdb=" O ARG E 33 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLN E 37 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU E 38 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TRP E 39 " --> pdb=" O SER E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 72 Processing helix chain 'E' and resid 112 through 129 Processing helix chain 'E' and resid 131 through 144 Processing helix chain 'E' and resid 189 through 204 Processing helix chain 'E' and resid 256 through 265 removed outlier: 3.622A pdb=" N ARG E 265 " --> pdb=" O GLY E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 285 No H-bonds generated for 'chain 'E' and resid 283 through 285' Processing helix chain 'E' and resid 303 through 313 Processing helix chain 'E' and resid 319 through 333 Processing helix chain 'F' and resid 32 through 36 removed outlier: 3.610A pdb=" N SER F 36 " --> pdb=" O ARG F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 73 removed outlier: 3.639A pdb=" N SER F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 129 removed outlier: 3.561A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 144 Processing helix chain 'F' and resid 190 through 204 removed outlier: 3.754A pdb=" N SER F 204 " --> pdb=" O ALA F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 removed outlier: 3.555A pdb=" N ILE F 260 " --> pdb=" O HIS F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 285 No H-bonds generated for 'chain 'F' and resid 283 through 285' Processing helix chain 'F' and resid 303 through 313 Processing helix chain 'F' and resid 319 through 333 Processing helix chain 'G' and resid 32 through 36 removed outlier: 3.527A pdb=" N SER G 36 " --> pdb=" O ARG G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 72 Processing helix chain 'G' and resid 111 through 129 Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 190 through 205 removed outlier: 3.510A pdb=" N GLY G 205 " --> pdb=" O SER G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 265 removed outlier: 3.528A pdb=" N ILE G 260 " --> pdb=" O HIS G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 313 Processing helix chain 'G' and resid 319 through 333 Processing helix chain 'H' and resid 32 through 36 removed outlier: 3.513A pdb=" N SER H 36 " --> pdb=" O ARG H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 73 removed outlier: 4.142A pdb=" N SER H 73 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 129 Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 189 through 204 Processing helix chain 'H' and resid 256 through 265 removed outlier: 3.527A pdb=" N ILE H 260 " --> pdb=" O HIS H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 274 through 278 Processing helix chain 'H' and resid 303 through 313 Processing helix chain 'H' and resid 319 through 333 Processing helix chain 'K' and resid 9 through 19 Processing helix chain 'K' and resid 57 through 68 Processing helix chain 'K' and resid 76 through 81 Processing helix chain 'K' and resid 81 through 86 Processing helix chain 'L' and resid 16 through 32 Processing helix chain 'L' and resid 33 through 35 No H-bonds generated for 'chain 'L' and resid 33 through 35' Processing helix chain 'L' and resid 67 through 71 removed outlier: 3.785A pdb=" N LEU L 70 " --> pdb=" O LEU L 67 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU L 71 " --> pdb=" O ARG L 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 67 through 71' Processing helix chain 'L' and resid 111 through 119 Processing helix chain 'L' and resid 123 through 131 removed outlier: 3.563A pdb=" N ALA L 127 " --> pdb=" O SER L 123 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 178 through 181 removed outlier: 8.610A pdb=" N ARG B 278 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU A 189 " --> pdb=" O ARG B 278 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B 280 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B 187 " --> pdb=" O GLU B 288 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181 removed outlier: 8.610A pdb=" N ARG B 278 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU A 189 " --> pdb=" O ARG B 278 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B 280 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N PHE B 279 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ALA B 257 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 251 " --> pdb=" O GLY B 285 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA B 253 " --> pdb=" O TRP B 316 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TRP B 316 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 313 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 232 removed outlier: 3.631A pdb=" N PHE A 232 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE B 219 " --> pdb=" O PHE A 232 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 239 through 241 Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 60 removed outlier: 5.773A pdb=" N GLY B 112 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 59 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU B 110 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ALA B 103 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLN B 18 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU B 105 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N SER B 16 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 107 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ARG B 14 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 65 through 68 removed outlier: 3.585A pdb=" N ARG B 65 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ALA B 103 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLN B 18 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU B 105 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N SER B 16 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 107 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ARG B 14 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B 157 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA8, first strand: chain 'C' and resid 108 through 109 removed outlier: 3.634A pdb=" N ALA C 108 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 12 " --> pdb=" O PHE C 336 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 19 through 20 Processing sheet with id=AB1, first strand: chain 'C' and resid 19 through 20 removed outlier: 4.533A pdb=" N VAL C 209 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 44 through 47 removed outlier: 3.616A pdb=" N LYS C 47 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL C 79 " --> pdb=" O LYS C 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 229 through 230 removed outlier: 4.156A pdb=" N THR C 245 " --> pdb=" O GLU C 230 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 248 through 249 removed outlier: 3.723A pdb=" N ALA C 252 " --> pdb=" O VAL C 249 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 266 through 268 removed outlier: 3.770A pdb=" N ILE C 280 " --> pdb=" O ASP C 268 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 12 through 13 removed outlier: 3.587A pdb=" N ALA D 108 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 19 through 20 removed outlier: 4.497A pdb=" N LEU D 210 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL D 160 " --> pdb=" O ARG D 175 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ARG D 175 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE D 162 " --> pdb=" O ALA D 173 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA D 173 " --> pdb=" O ILE D 162 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS D 164 " --> pdb=" O ALA D 171 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 19 through 20 Processing sheet with id=AB9, first strand: chain 'D' and resid 45 through 51 removed outlier: 3.991A pdb=" N GLY D 51 " --> pdb=" O ASN D 75 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASN D 75 " --> pdb=" O GLY D 51 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 229 through 230 removed outlier: 4.539A pdb=" N THR D 245 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 287 through 288 removed outlier: 3.579A pdb=" N LYS D 293 " --> pdb=" O VAL D 288 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 108 through 109 removed outlier: 3.574A pdb=" N LEU E 12 " --> pdb=" O PHE E 336 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 19 through 20 removed outlier: 3.541A pdb=" N VAL E 99 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL E 209 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LEU E 210 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL E 160 " --> pdb=" O ARG E 175 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ARG E 175 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE E 162 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ALA E 173 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N HIS E 164 " --> pdb=" O ALA E 171 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 19 through 20 removed outlier: 3.547A pdb=" N ARG E 94 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA E 253 " --> pdb=" O MET E 25 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA E 252 " --> pdb=" O VAL E 249 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 45 through 50 Processing sheet with id=AC7, first strand: chain 'E' and resid 266 through 268 Processing sheet with id=AC8, first strand: chain 'E' and resid 287 through 288 Processing sheet with id=AC9, first strand: chain 'F' and resid 108 through 109 removed outlier: 3.581A pdb=" N ALA F 108 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU F 12 " --> pdb=" O PHE F 336 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 19 through 20 removed outlier: 4.492A pdb=" N VAL F 209 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU F 210 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA F 157 " --> pdb=" O ARG F 218 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL F 158 " --> pdb=" O ASP F 177 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASP F 177 " --> pdb=" O VAL F 158 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL F 160 " --> pdb=" O ARG F 175 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG F 175 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE F 162 " --> pdb=" O ALA F 173 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ALA F 173 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N HIS F 164 " --> pdb=" O ALA F 171 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 19 through 20 Processing sheet with id=AD3, first strand: chain 'F' and resid 45 through 50 removed outlier: 4.572A pdb=" N ALA F 82 " --> pdb=" O VAL F 225 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 266 through 268 Processing sheet with id=AD5, first strand: chain 'F' and resid 287 through 288 Processing sheet with id=AD6, first strand: chain 'G' and resid 12 through 14 Processing sheet with id=AD7, first strand: chain 'G' and resid 19 through 20 removed outlier: 4.352A pdb=" N VAL G 209 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU G 210 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA G 157 " --> pdb=" O ARG G 218 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL G 160 " --> pdb=" O PHE G 176 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG G 172 " --> pdb=" O HIS G 164 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 19 through 20 removed outlier: 4.861A pdb=" N ALA G 253 " --> pdb=" O MET G 25 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA G 252 " --> pdb=" O VAL G 249 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 45 through 50 removed outlier: 4.502A pdb=" N ALA G 82 " --> pdb=" O VAL G 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 45 through 50 removed outlier: 7.618A pdb=" N SER G 243 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N THR G 78 " --> pdb=" O SER G 243 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 108 through 109 removed outlier: 3.804A pdb=" N LEU H 12 " --> pdb=" O PHE H 336 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 19 through 20 removed outlier: 4.456A pdb=" N VAL H 209 " --> pdb=" O VAL H 99 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 170 through 177 removed outlier: 3.557A pdb=" N ARG H 172 " --> pdb=" O HIS H 164 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA H 157 " --> pdb=" O ARG H 218 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ALA H 253 " --> pdb=" O MET H 25 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL H 249 " --> pdb=" O ALA H 252 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 44 through 50 removed outlier: 4.413A pdb=" N ALA H 82 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 44 through 50 removed outlier: 7.524A pdb=" N SER H 243 " --> pdb=" O LEU H 76 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N THR H 78 " --> pdb=" O SER H 243 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 266 through 268 Processing sheet with id=AE8, first strand: chain 'H' and resid 287 through 288 Processing sheet with id=AE9, first strand: chain 'K' and resid 23 through 27 Processing sheet with id=AF1, first strand: chain 'K' and resid 41 through 46 removed outlier: 3.628A pdb=" N ILE K 44 " --> pdb=" O TYR K 51 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 5 through 6 926 hydrogen bonds defined for protein. 2586 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3 hydrogen bonds 6 hydrogen bond angles 0 basepair planarities 1 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 4.22 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4584 1.32 - 1.45: 5677 1.45 - 1.57: 12320 1.57 - 1.69: 118 1.69 - 1.81: 30 Bond restraints: 22729 Sorted by residual: bond pdb=" C LEU B 181 " pdb=" N PRO B 182 " ideal model delta sigma weight residual 1.331 1.364 -0.033 7.90e-03 1.60e+04 1.72e+01 bond pdb=" C PHE B 152 " pdb=" N PRO B 153 " ideal model delta sigma weight residual 1.339 1.448 -0.109 3.40e-02 8.65e+02 1.03e+01 bond pdb=" CG1 ILE E 260 " pdb=" CD1 ILE E 260 " ideal model delta sigma weight residual 1.513 1.402 0.111 3.90e-02 6.57e+02 8.09e+00 bond pdb=" CG1 ILE F 260 " pdb=" CD1 ILE F 260 " ideal model delta sigma weight residual 1.513 1.408 0.105 3.90e-02 6.57e+02 7.31e+00 bond pdb=" C ARG B 85 " pdb=" N ASN B 86 " ideal model delta sigma weight residual 1.329 1.281 0.048 1.86e-02 2.89e+03 6.66e+00 ... (remaining 22724 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 29525 2.27 - 4.54: 1214 4.54 - 6.81: 143 6.81 - 9.08: 34 9.08 - 11.35: 6 Bond angle restraints: 30922 Sorted by residual: angle pdb=" N GLN G 37 " pdb=" CA GLN G 37 " pdb=" C GLN G 37 " ideal model delta sigma weight residual 114.56 106.99 7.57 1.27e+00 6.20e-01 3.55e+01 angle pdb=" C SER A 252 " pdb=" N GLN A 253 " pdb=" CA GLN A 253 " ideal model delta sigma weight residual 122.08 130.02 -7.94 1.47e+00 4.63e-01 2.91e+01 angle pdb=" C LYS H 58 " pdb=" N THR H 59 " pdb=" CA THR H 59 " ideal model delta sigma weight residual 122.61 129.57 -6.96 1.56e+00 4.11e-01 1.99e+01 angle pdb=" C GLN G 32 " pdb=" N ARG G 33 " pdb=" CA ARG G 33 " ideal model delta sigma weight residual 120.38 126.82 -6.44 1.46e+00 4.69e-01 1.95e+01 angle pdb=" N GLN D 167 " pdb=" CA GLN D 167 " pdb=" C GLN D 167 " ideal model delta sigma weight residual 108.07 102.02 6.05 1.38e+00 5.25e-01 1.92e+01 ... (remaining 30917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.59: 12665 32.59 - 65.18: 313 65.18 - 97.77: 29 97.77 - 130.36: 0 130.36 - 162.95: 2 Dihedral angle restraints: 13009 sinusoidal: 5442 harmonic: 7567 Sorted by residual: dihedral pdb=" O4' U M 43 " pdb=" C1' U M 43 " pdb=" N1 U M 43 " pdb=" C2 U M 43 " ideal model delta sinusoidal sigma weight residual 200.00 37.05 162.95 1 1.50e+01 4.44e-03 8.35e+01 dihedral pdb=" CA TYR E 285 " pdb=" C TYR E 285 " pdb=" N GLY E 286 " pdb=" CA GLY E 286 " ideal model delta harmonic sigma weight residual 180.00 -136.39 -43.61 0 5.00e+00 4.00e-02 7.61e+01 dihedral pdb=" O4' U M 21 " pdb=" C1' U M 21 " pdb=" N1 U M 21 " pdb=" C2 U M 21 " ideal model delta sinusoidal sigma weight residual 200.00 69.00 131.00 1 1.50e+01 4.44e-03 7.07e+01 ... (remaining 13006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2633 0.076 - 0.152: 539 0.152 - 0.228: 38 0.228 - 0.304: 3 0.304 - 0.381: 2 Chirality restraints: 3215 Sorted by residual: chirality pdb=" CB ILE H 267 " pdb=" CA ILE H 267 " pdb=" CG1 ILE H 267 " pdb=" CG2 ILE H 267 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CB ILE F 267 " pdb=" CA ILE F 267 " pdb=" CG1 ILE F 267 " pdb=" CG2 ILE F 267 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C1' U M 21 " pdb=" O4' U M 21 " pdb=" C2' U M 21 " pdb=" N1 U M 21 " both_signs ideal model delta sigma weight residual False 2.47 2.20 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 3212 not shown) Planarity restraints: 4018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 311 " -0.030 2.00e-02 2.50e+03 2.35e-02 1.38e+01 pdb=" CG TRP E 311 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP E 311 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP E 311 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 311 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP E 311 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 311 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 311 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 311 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E 311 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 311 " -0.028 2.00e-02 2.50e+03 2.15e-02 1.16e+01 pdb=" CG TRP D 311 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP D 311 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP D 311 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 311 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP D 311 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP D 311 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 311 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 311 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 311 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 311 " 0.027 2.00e-02 2.50e+03 2.10e-02 1.10e+01 pdb=" CG TRP G 311 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP G 311 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP G 311 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP G 311 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP G 311 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP G 311 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 311 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 311 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP G 311 " 0.001 2.00e-02 2.50e+03 ... (remaining 4015 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 770 2.69 - 3.24: 20059 3.24 - 3.79: 34769 3.79 - 4.35: 46103 4.35 - 4.90: 76746 Nonbonded interactions: 178447 Sorted by model distance: nonbonded pdb=" CB ALA L 0 " pdb=" N GLU L 170 " model vdw 2.133 3.540 nonbonded pdb=" OH TYR E 305 " pdb=" O SER F 54 " model vdw 2.278 3.040 nonbonded pdb=" O GLU E 283 " pdb=" OH TYR E 325 " model vdw 2.285 3.040 nonbonded pdb=" OH TYR C 271 " pdb=" O GLY C 278 " model vdw 2.285 3.040 nonbonded pdb=" OH TYR F 305 " pdb=" O SER G 54 " model vdw 2.286 3.040 ... (remaining 178442 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 'C' and (resid 6 through 272 or (resid 273 through 275 and (name N or nam \ e CA or name C or name O or name CB )) or resid 276 through 338)) selection = (chain 'D' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'E' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'F' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'G' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'H' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) } 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.970 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 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 : 0.010 0.389 22730 Z= 0.473 Angle : 1.034 11.348 30922 Z= 0.570 Chirality : 0.059 0.381 3215 Planarity : 0.006 0.061 4018 Dihedral : 13.370 162.947 8459 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.65 % Favored : 89.18 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.03 (0.12), residues: 2939 helix: -2.54 (0.13), residues: 885 sheet: -1.24 (0.24), residues: 439 loop : -3.29 (0.12), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG B 102 TYR 0.036 0.004 TYR D 305 PHE 0.027 0.004 PHE C 216 TRP 0.064 0.006 TRP E 311 HIS 0.020 0.004 HIS F 164 Details of bonding type rmsd covalent geometry : bond 0.00920 (22729) covalent geometry : angle 1.03389 (30922) hydrogen bonds : bond 0.18535 ( 897) hydrogen bonds : angle 8.40107 ( 2592) Misc. bond : bond 0.38922 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 494 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ARG cc_start: 0.6502 (ttm110) cc_final: 0.6270 (ttm110) REVERT: B 108 SER cc_start: 0.7328 (m) cc_final: 0.6689 (p) REVERT: B 116 ASP cc_start: 0.5717 (p0) cc_final: 0.5095 (m-30) REVERT: C 124 THR cc_start: 0.8030 (m) cc_final: 0.7277 (m) REVERT: D 221 ASP cc_start: 0.7063 (m-30) cc_final: 0.6862 (m-30) REVERT: D 302 LEU cc_start: 0.7323 (mt) cc_final: 0.7006 (mt) REVERT: G 119 LEU cc_start: 0.8563 (mt) cc_final: 0.8327 (mt) outliers start: 0 outliers final: 0 residues processed: 494 average time/residue: 0.1951 time to fit residues: 139.3455 Evaluate side-chains 236 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 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 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 HIS B 42 HIS C 110 ASN C 129 GLN C 164 HIS D 164 HIS D 262 ASN E 164 HIS E 329 ASN F 75 ASN F 164 HIS F 256 HIS F 291 GLN H 32 GLN H 129 GLN H 164 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.140631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.100478 restraints weight = 35020.963| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.64 r_work: 0.3085 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22730 Z= 0.146 Angle : 0.642 11.931 30922 Z= 0.342 Chirality : 0.042 0.209 3215 Planarity : 0.005 0.064 4018 Dihedral : 14.286 157.546 4141 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 1.93 % Allowed : 8.46 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.14), residues: 2939 helix: -0.45 (0.16), residues: 930 sheet: -0.44 (0.24), residues: 451 loop : -2.85 (0.14), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 218 TYR 0.022 0.002 TYR C 114 PHE 0.018 0.002 PHE B 184 TRP 0.021 0.002 TRP G 311 HIS 0.008 0.002 HIS D 324 Details of bonding type rmsd covalent geometry : bond 0.00307 (22729) covalent geometry : angle 0.64198 (30922) hydrogen bonds : bond 0.03481 ( 897) hydrogen bonds : angle 5.15926 ( 2592) Misc. bond : bond 0.00458 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 271 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 HIS cc_start: 0.8094 (t-90) cc_final: 0.7825 (t70) REVERT: A 222 ARG cc_start: 0.6653 (mmm-85) cc_final: 0.6173 (mmm-85) REVERT: B 124 GLN cc_start: 0.7288 (tp-100) cc_final: 0.7008 (pm20) REVERT: D 270 TRP cc_start: 0.8320 (OUTLIER) cc_final: 0.8101 (p90) REVERT: F 34 ASP cc_start: 0.6991 (m-30) cc_final: 0.6574 (m-30) REVERT: G 119 LEU cc_start: 0.8908 (mt) cc_final: 0.8650 (mt) REVERT: H 119 LEU cc_start: 0.8942 (mm) cc_final: 0.8626 (mm) REVERT: K 53 MET cc_start: 0.5957 (tmm) cc_final: 0.5744 (tmm) outliers start: 37 outliers final: 18 residues processed: 296 average time/residue: 0.1883 time to fit residues: 81.5007 Evaluate side-chains 202 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 270 TRP Chi-restraints excluded: chain E residue 129 GLN Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 267 optimal weight: 20.0000 chunk 240 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 219 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 12 optimal weight: 40.0000 chunk 140 optimal weight: 0.0570 chunk 30 optimal weight: 50.0000 chunk 120 optimal weight: 2.9990 chunk 17 optimal weight: 0.0030 overall best weight: 1.4112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 200 HIS A 249 GLN B 18 GLN B 133 GLN B 256 ASN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 ASN D 262 ASN F 208 HIS F 256 HIS G 110 ASN G 151 ASN H 32 GLN H 329 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.137858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.096750 restraints weight = 34799.923| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.72 r_work: 0.3004 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.5636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 22730 Z= 0.164 Angle : 0.622 11.749 30922 Z= 0.327 Chirality : 0.042 0.194 3215 Planarity : 0.004 0.055 4018 Dihedral : 14.098 156.800 4141 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 2.30 % Allowed : 11.17 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.15), residues: 2939 helix: 0.47 (0.17), residues: 935 sheet: 0.03 (0.25), residues: 428 loop : -2.51 (0.14), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 172 TYR 0.020 0.002 TYR C 114 PHE 0.017 0.002 PHE B 184 TRP 0.025 0.002 TRP D 174 HIS 0.011 0.001 HIS F 256 Details of bonding type rmsd covalent geometry : bond 0.00371 (22729) covalent geometry : angle 0.62157 (30922) hydrogen bonds : bond 0.03851 ( 897) hydrogen bonds : angle 4.75856 ( 2592) Misc. bond : bond 0.00057 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 HIS cc_start: 0.8380 (t70) cc_final: 0.7881 (t70) REVERT: B 133 GLN cc_start: 0.8930 (tp-100) cc_final: 0.8630 (tp-100) REVERT: B 321 PHE cc_start: 0.5031 (t80) cc_final: 0.4773 (t80) REVERT: C 247 TYR cc_start: 0.8009 (t80) cc_final: 0.7792 (t80) REVERT: C 293 LYS cc_start: 0.8152 (ttmt) cc_final: 0.7487 (tmtt) REVERT: D 44 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8348 (t) REVERT: D 193 ASP cc_start: 0.8729 (m-30) cc_final: 0.8482 (m-30) REVERT: D 283 GLU cc_start: 0.8292 (mm-30) cc_final: 0.8053 (mt-10) REVERT: E 114 TYR cc_start: 0.9001 (t80) cc_final: 0.8772 (t80) REVERT: F 245 THR cc_start: 0.9271 (t) cc_final: 0.9026 (m) REVERT: G 119 LEU cc_start: 0.9227 (mt) cc_final: 0.8919 (mt) REVERT: G 241 GLN cc_start: 0.8080 (pm20) cc_final: 0.6894 (tt0) REVERT: H 119 LEU cc_start: 0.9061 (mm) cc_final: 0.8588 (mm) REVERT: H 271 TYR cc_start: 0.8988 (p90) cc_final: 0.8736 (p90) REVERT: K 53 MET cc_start: 0.6487 (tmm) cc_final: 0.6093 (tmm) outliers start: 44 outliers final: 27 residues processed: 240 average time/residue: 0.2017 time to fit residues: 69.8478 Evaluate side-chains 172 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 129 GLN Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain G residue 151 ASN Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 48 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 178 optimal weight: 0.6980 chunk 277 optimal weight: 50.0000 chunk 181 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 264 optimal weight: 7.9990 chunk 218 optimal weight: 2.9990 chunk 295 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 chunk 272 optimal weight: 2.9990 chunk 177 optimal weight: 8.9990 chunk 259 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 HIS A 241 GLN A 249 GLN B 129 GLN B 173 GLN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 ASN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN G 329 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.135611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.095287 restraints weight = 35273.443| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.11 r_work: 0.2972 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.6258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22730 Z= 0.162 Angle : 0.575 13.838 30922 Z= 0.303 Chirality : 0.041 0.194 3215 Planarity : 0.004 0.041 4018 Dihedral : 14.007 157.596 4141 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 1.93 % Allowed : 11.96 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.15), residues: 2939 helix: 1.00 (0.17), residues: 930 sheet: 0.27 (0.26), residues: 431 loop : -2.34 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 184 TYR 0.021 0.002 TYR K 64 PHE 0.015 0.001 PHE B 184 TRP 0.028 0.002 TRP B 147 HIS 0.005 0.001 HIS H 324 Details of bonding type rmsd covalent geometry : bond 0.00370 (22729) covalent geometry : angle 0.57505 (30922) hydrogen bonds : bond 0.03210 ( 897) hydrogen bonds : angle 4.52684 ( 2592) Misc. bond : bond 0.00356 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 SER cc_start: 0.9039 (p) cc_final: 0.8786 (t) REVERT: A 222 ARG cc_start: 0.6488 (mmm-85) cc_final: 0.6130 (mmm-85) REVERT: B 97 ILE cc_start: 0.9009 (mt) cc_final: 0.8804 (mt) REVERT: B 99 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: C 293 LYS cc_start: 0.8183 (ttmt) cc_final: 0.7547 (tmtt) REVERT: D 44 VAL cc_start: 0.8827 (OUTLIER) cc_final: 0.8438 (t) REVERT: D 50 ARG cc_start: 0.7668 (ttp80) cc_final: 0.7124 (ptt180) REVERT: D 193 ASP cc_start: 0.8815 (m-30) cc_final: 0.8594 (m-30) REVERT: E 74 PRO cc_start: 0.8137 (Cg_endo) cc_final: 0.7916 (Cg_exo) REVERT: F 245 THR cc_start: 0.9262 (t) cc_final: 0.9041 (m) REVERT: G 241 GLN cc_start: 0.8080 (pm20) cc_final: 0.6906 (tt0) REVERT: H 119 LEU cc_start: 0.9127 (mm) cc_final: 0.8603 (mm) outliers start: 37 outliers final: 26 residues processed: 192 average time/residue: 0.1974 time to fit residues: 55.5090 Evaluate side-chains 170 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 232 ILE Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain K residue 38 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 57 optimal weight: 0.1980 chunk 232 optimal weight: 0.9980 chunk 253 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 260 optimal weight: 4.9990 chunk 85 optimal weight: 0.0000 chunk 230 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 0 optimal weight: 60.0000 chunk 269 optimal weight: 6.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS B 306 HIS C 83 ASN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN G 141 ASN G 151 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.135865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.095706 restraints weight = 35029.527| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.24 r_work: 0.2970 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.6675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22730 Z= 0.142 Angle : 0.551 12.477 30922 Z= 0.290 Chirality : 0.041 0.240 3215 Planarity : 0.004 0.038 4018 Dihedral : 13.882 157.779 4141 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 2.09 % Allowed : 12.95 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.16), residues: 2939 helix: 1.36 (0.18), residues: 928 sheet: 0.33 (0.26), residues: 431 loop : -2.24 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 172 TYR 0.019 0.001 TYR C 114 PHE 0.014 0.001 PHE B 184 TRP 0.020 0.002 TRP B 147 HIS 0.004 0.001 HIS D 324 Details of bonding type rmsd covalent geometry : bond 0.00321 (22729) covalent geometry : angle 0.55125 (30922) hydrogen bonds : bond 0.03156 ( 897) hydrogen bonds : angle 4.38113 ( 2592) Misc. bond : bond 0.00127 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.6674 (mmm-85) cc_final: 0.6217 (mmm-85) REVERT: B 99 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: C 247 TYR cc_start: 0.8120 (t80) cc_final: 0.7838 (t80) REVERT: C 293 LYS cc_start: 0.8208 (ttmt) cc_final: 0.7581 (tmtt) REVERT: D 44 VAL cc_start: 0.8894 (OUTLIER) cc_final: 0.8478 (t) REVERT: D 50 ARG cc_start: 0.7772 (ttp80) cc_final: 0.7320 (ptt180) REVERT: D 193 ASP cc_start: 0.8834 (m-30) cc_final: 0.8588 (m-30) REVERT: E 74 PRO cc_start: 0.8164 (Cg_endo) cc_final: 0.7866 (Cg_exo) REVERT: E 75 ASN cc_start: 0.8068 (t0) cc_final: 0.7794 (p0) REVERT: G 241 GLN cc_start: 0.8071 (pm20) cc_final: 0.7036 (tt0) REVERT: H 119 LEU cc_start: 0.9146 (mm) cc_final: 0.8594 (mm) REVERT: H 271 TYR cc_start: 0.9145 (p90) cc_final: 0.8927 (p90) outliers start: 40 outliers final: 27 residues processed: 190 average time/residue: 0.1873 time to fit residues: 53.1692 Evaluate side-chains 167 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain G residue 50 ARG Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 232 ILE Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain K residue 38 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 42 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 231 optimal weight: 0.0870 chunk 126 optimal weight: 0.7980 chunk 269 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 158 optimal weight: 0.6980 chunk 194 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 GLN A 249 GLN B 18 GLN B 114 HIS B 282 ASN C 83 ASN F 72 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.138113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.097748 restraints weight = 35188.597| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.62 r_work: 0.3037 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.6940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 22730 Z= 0.100 Angle : 0.506 11.726 30922 Z= 0.266 Chirality : 0.039 0.250 3215 Planarity : 0.003 0.038 4018 Dihedral : 13.819 157.523 4141 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.88 % Allowed : 13.79 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.16), residues: 2939 helix: 1.71 (0.18), residues: 923 sheet: 0.40 (0.26), residues: 431 loop : -2.15 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 172 TYR 0.018 0.001 TYR C 114 PHE 0.014 0.001 PHE A 211 TRP 0.016 0.001 TRP B 147 HIS 0.005 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00218 (22729) covalent geometry : angle 0.50649 (30922) hydrogen bonds : bond 0.02834 ( 897) hydrogen bonds : angle 4.16871 ( 2592) Misc. bond : bond 0.00218 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: B 161 MET cc_start: 0.6749 (pmm) cc_final: 0.6044 (pmm) REVERT: C 293 LYS cc_start: 0.7948 (ttmt) cc_final: 0.7494 (tmtt) REVERT: D 44 VAL cc_start: 0.8839 (OUTLIER) cc_final: 0.8446 (t) REVERT: D 50 ARG cc_start: 0.7875 (ttp80) cc_final: 0.7443 (ptt180) REVERT: D 193 ASP cc_start: 0.8721 (m-30) cc_final: 0.8481 (m-30) REVERT: E 74 PRO cc_start: 0.8179 (Cg_endo) cc_final: 0.7861 (Cg_exo) REVERT: E 75 ASN cc_start: 0.7982 (t0) cc_final: 0.7734 (p0) REVERT: F 295 TYR cc_start: 0.8807 (m-80) cc_final: 0.8559 (m-80) REVERT: G 241 GLN cc_start: 0.7974 (pm20) cc_final: 0.6886 (tt0) REVERT: H 119 LEU cc_start: 0.9134 (mm) cc_final: 0.8570 (mm) outliers start: 36 outliers final: 24 residues processed: 200 average time/residue: 0.1858 time to fit residues: 55.3678 Evaluate side-chains 173 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain G residue 50 ARG Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 232 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 56 optimal weight: 8.9990 chunk 162 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 231 optimal weight: 0.0970 chunk 188 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 chunk 72 optimal weight: 0.0060 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN C 83 ASN E 329 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.138526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.097479 restraints weight = 34892.788| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.84 r_work: 0.3040 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.7107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 22730 Z= 0.101 Angle : 0.500 11.478 30922 Z= 0.263 Chirality : 0.039 0.236 3215 Planarity : 0.003 0.034 4018 Dihedral : 13.765 157.565 4141 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.09 % Allowed : 13.73 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.16), residues: 2939 helix: 1.80 (0.18), residues: 942 sheet: 0.44 (0.26), residues: 433 loop : -2.10 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 172 TYR 0.017 0.001 TYR C 305 PHE 0.010 0.001 PHE B 184 TRP 0.014 0.001 TRP B 147 HIS 0.004 0.001 HIS F 324 Details of bonding type rmsd covalent geometry : bond 0.00220 (22729) covalent geometry : angle 0.49987 (30922) hydrogen bonds : bond 0.02788 ( 897) hydrogen bonds : angle 4.05621 ( 2592) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 HIS cc_start: 0.8521 (t70) cc_final: 0.8073 (t70) REVERT: A 235 TYR cc_start: 0.8069 (m-80) cc_final: 0.7838 (m-80) REVERT: B 99 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: B 161 MET cc_start: 0.6670 (pmm) cc_final: 0.6036 (pmm) REVERT: C 247 TYR cc_start: 0.8279 (t80) cc_final: 0.8053 (t80) REVERT: C 293 LYS cc_start: 0.8011 (ttmt) cc_final: 0.7571 (tmtt) REVERT: D 44 VAL cc_start: 0.8784 (OUTLIER) cc_final: 0.8382 (t) REVERT: D 50 ARG cc_start: 0.7844 (ttp80) cc_final: 0.7457 (ptt180) REVERT: D 193 ASP cc_start: 0.8720 (m-30) cc_final: 0.8485 (m-30) REVERT: E 66 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8467 (mtmm) REVERT: E 74 PRO cc_start: 0.8190 (Cg_endo) cc_final: 0.7866 (Cg_exo) REVERT: E 75 ASN cc_start: 0.8033 (t0) cc_final: 0.7754 (p0) REVERT: G 33 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8586 (ptt-90) REVERT: G 241 GLN cc_start: 0.7869 (pm20) cc_final: 0.6775 (tt0) REVERT: H 119 LEU cc_start: 0.9135 (mm) cc_final: 0.8587 (mm) REVERT: H 271 TYR cc_start: 0.9131 (p90) cc_final: 0.8888 (p90) REVERT: K 53 MET cc_start: 0.4875 (ppp) cc_final: 0.4547 (ppp) outliers start: 40 outliers final: 28 residues processed: 190 average time/residue: 0.1939 time to fit residues: 54.2577 Evaluate side-chains 176 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain G residue 33 ARG Chi-restraints excluded: chain G residue 50 ARG Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 232 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 30 optimal weight: 50.0000 chunk 276 optimal weight: 50.0000 chunk 173 optimal weight: 0.4980 chunk 149 optimal weight: 0.8980 chunk 258 optimal weight: 2.9990 chunk 295 optimal weight: 8.9990 chunk 0 optimal weight: 70.0000 chunk 192 optimal weight: 4.9990 chunk 228 optimal weight: 0.0470 chunk 47 optimal weight: 6.9990 chunk 223 optimal weight: 0.0000 overall best weight: 0.8884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS B 282 ASN C 83 ASN C 129 GLN ** C 140 HIS ** 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 = 0.3800 r_free = 0.3800 target = 0.138286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.097173 restraints weight = 34911.379| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.89 r_work: 0.3014 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.7250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 22730 Z= 0.108 Angle : 0.511 11.365 30922 Z= 0.267 Chirality : 0.040 0.230 3215 Planarity : 0.003 0.032 4018 Dihedral : 13.738 157.569 4141 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 1.78 % Allowed : 14.36 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.16), residues: 2939 helix: 1.93 (0.18), residues: 936 sheet: 0.48 (0.26), residues: 433 loop : -2.05 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 172 TYR 0.018 0.001 TYR C 305 PHE 0.012 0.001 PHE B 284 TRP 0.012 0.001 TRP B 147 HIS 0.003 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00240 (22729) covalent geometry : angle 0.51134 (30922) hydrogen bonds : bond 0.02802 ( 897) hydrogen bonds : angle 4.02128 ( 2592) Misc. bond : bond 0.00084 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 HIS cc_start: 0.8551 (t70) cc_final: 0.8102 (t70) REVERT: A 235 TYR cc_start: 0.8029 (m-80) cc_final: 0.7760 (m-80) REVERT: B 99 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: C 231 LEU cc_start: 0.8543 (tp) cc_final: 0.8329 (tp) REVERT: C 293 LYS cc_start: 0.8108 (ttmt) cc_final: 0.7647 (tmtt) REVERT: D 44 VAL cc_start: 0.8810 (OUTLIER) cc_final: 0.8378 (t) REVERT: D 50 ARG cc_start: 0.7896 (ttp80) cc_final: 0.7444 (ptt180) REVERT: D 193 ASP cc_start: 0.8720 (m-30) cc_final: 0.8499 (m-30) REVERT: E 66 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8522 (mtmm) REVERT: E 74 PRO cc_start: 0.8197 (Cg_endo) cc_final: 0.7876 (Cg_exo) REVERT: F 38 GLU cc_start: 0.8387 (pm20) cc_final: 0.7986 (pp20) REVERT: F 295 TYR cc_start: 0.8826 (m-80) cc_final: 0.8551 (m-80) REVERT: G 241 GLN cc_start: 0.7836 (pm20) cc_final: 0.6850 (tt0) REVERT: H 119 LEU cc_start: 0.9131 (mm) cc_final: 0.8600 (mm) REVERT: H 250 ARG cc_start: 0.7859 (ptp90) cc_final: 0.7550 (ptt180) REVERT: K 53 MET cc_start: 0.4973 (ppp) cc_final: 0.4686 (ppp) outliers start: 34 outliers final: 28 residues processed: 176 average time/residue: 0.1908 time to fit residues: 49.7699 Evaluate side-chains 169 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 110 ASN Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 232 ILE Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 276 optimal weight: 50.0000 chunk 239 optimal weight: 0.0770 chunk 156 optimal weight: 0.9980 chunk 258 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 223 optimal weight: 0.1980 chunk 187 optimal weight: 0.1980 chunk 250 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN C 83 ASN H 164 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.140102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.099840 restraints weight = 34786.762| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.00 r_work: 0.3058 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.7411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 22730 Z= 0.089 Angle : 0.494 11.524 30922 Z= 0.257 Chirality : 0.039 0.229 3215 Planarity : 0.003 0.033 4018 Dihedral : 13.708 157.510 4141 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.57 % Allowed : 14.67 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.16), residues: 2939 helix: 2.09 (0.18), residues: 935 sheet: 0.49 (0.25), residues: 441 loop : -2.01 (0.15), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 172 TYR 0.015 0.001 TYR C 114 PHE 0.008 0.001 PHE B 184 TRP 0.012 0.001 TRP B 147 HIS 0.004 0.001 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00190 (22729) covalent geometry : angle 0.49391 (30922) hydrogen bonds : bond 0.02650 ( 897) hydrogen bonds : angle 3.88769 ( 2592) Misc. bond : bond 0.00067 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 HIS cc_start: 0.8417 (t70) cc_final: 0.7943 (t70) REVERT: A 222 ARG cc_start: 0.6745 (mmm-85) cc_final: 0.5861 (mpt180) REVERT: A 259 ARG cc_start: 0.8029 (mmt90) cc_final: 0.7810 (mpp-170) REVERT: B 99 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: B 150 GLU cc_start: 0.6794 (mm-30) cc_final: 0.6573 (tp30) REVERT: C 186 PHE cc_start: 0.4972 (m-10) cc_final: 0.4709 (m-10) REVERT: C 293 LYS cc_start: 0.8011 (ttmt) cc_final: 0.7626 (tmtt) REVERT: D 44 VAL cc_start: 0.8750 (OUTLIER) cc_final: 0.8332 (t) REVERT: D 50 ARG cc_start: 0.7862 (ttp80) cc_final: 0.7487 (ptt180) REVERT: D 193 ASP cc_start: 0.8775 (m-30) cc_final: 0.8560 (m-30) REVERT: E 66 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8535 (mtmm) REVERT: F 38 GLU cc_start: 0.8327 (pm20) cc_final: 0.7934 (pp20) REVERT: F 295 TYR cc_start: 0.8811 (m-80) cc_final: 0.8489 (m-80) REVERT: G 241 GLN cc_start: 0.7818 (pm20) cc_final: 0.7007 (tt0) REVERT: H 247 TYR cc_start: 0.9319 (t80) cc_final: 0.9073 (t80) REVERT: H 271 TYR cc_start: 0.9118 (p90) cc_final: 0.8837 (p90) REVERT: K 1 MET cc_start: 0.3660 (ptm) cc_final: 0.0992 (tpt) REVERT: K 32 TYR cc_start: 0.8152 (m-10) cc_final: 0.7746 (m-80) outliers start: 30 outliers final: 23 residues processed: 184 average time/residue: 0.1928 time to fit residues: 52.7231 Evaluate side-chains 172 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 243 optimal weight: 8.9990 chunk 175 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 198 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 189 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 8 optimal weight: 20.0000 chunk 226 optimal weight: 1.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 HIS B 114 HIS B 282 ASN B 306 HIS C 83 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.137398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.093814 restraints weight = 34868.144| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.37 r_work: 0.3012 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.7496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22730 Z= 0.123 Angle : 0.528 11.438 30922 Z= 0.274 Chirality : 0.040 0.219 3215 Planarity : 0.003 0.035 4018 Dihedral : 13.676 157.511 4141 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.51 % Allowed : 15.09 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.16), residues: 2939 helix: 2.03 (0.18), residues: 936 sheet: 0.58 (0.26), residues: 434 loop : -1.97 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 184 TYR 0.023 0.001 TYR C 305 PHE 0.013 0.001 PHE B 284 TRP 0.013 0.001 TRP F 311 HIS 0.004 0.001 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00278 (22729) covalent geometry : angle 0.52753 (30922) hydrogen bonds : bond 0.02898 ( 897) hydrogen bonds : angle 3.95499 ( 2592) Misc. bond : bond 0.00069 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 HIS cc_start: 0.8445 (t70) cc_final: 0.7983 (t70) REVERT: A 259 ARG cc_start: 0.8091 (mmt90) cc_final: 0.7800 (mpp-170) REVERT: B 99 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: B 150 GLU cc_start: 0.6743 (mm-30) cc_final: 0.6494 (tp30) REVERT: C 176 PHE cc_start: 0.7719 (m-10) cc_final: 0.7470 (m-10) REVERT: C 283 GLU cc_start: 0.8611 (pm20) cc_final: 0.7817 (pm20) REVERT: C 293 LYS cc_start: 0.8135 (ttmt) cc_final: 0.7645 (tmtt) REVERT: D 50 ARG cc_start: 0.7929 (ttp80) cc_final: 0.7622 (ptt180) REVERT: D 193 ASP cc_start: 0.8753 (m-30) cc_final: 0.8538 (m-30) REVERT: E 66 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8579 (mtmm) REVERT: F 38 GLU cc_start: 0.8332 (pm20) cc_final: 0.7942 (pp20) REVERT: F 295 TYR cc_start: 0.8831 (m-80) cc_final: 0.8547 (m-80) REVERT: G 241 GLN cc_start: 0.7842 (pm20) cc_final: 0.7029 (tt0) REVERT: H 66 LYS cc_start: 0.8622 (mmmt) cc_final: 0.8263 (mmmt) REVERT: H 119 LEU cc_start: 0.9138 (mm) cc_final: 0.8615 (mm) REVERT: H 250 ARG cc_start: 0.7855 (ptp90) cc_final: 0.7533 (ptt180) REVERT: H 271 TYR cc_start: 0.9199 (p90) cc_final: 0.8996 (p90) REVERT: K 1 MET cc_start: 0.3730 (ptm) cc_final: 0.1040 (tpt) REVERT: K 32 TYR cc_start: 0.8170 (m-10) cc_final: 0.7775 (m-80) outliers start: 29 outliers final: 26 residues processed: 171 average time/residue: 0.1901 time to fit residues: 48.6272 Evaluate side-chains 171 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 14 optimal weight: 60.0000 chunk 198 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 124 optimal weight: 0.2980 chunk 219 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 10 optimal weight: 40.0000 chunk 146 optimal weight: 0.8980 chunk 154 optimal weight: 0.6980 chunk 170 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 HIS B 282 ASN C 83 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.138555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.095988 restraints weight = 35025.262| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.92 r_work: 0.3009 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.7565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 22730 Z= 0.102 Angle : 0.510 11.412 30922 Z= 0.266 Chirality : 0.039 0.225 3215 Planarity : 0.003 0.034 4018 Dihedral : 13.674 157.463 4141 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.41 % Allowed : 15.14 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.16), residues: 2939 helix: 2.08 (0.18), residues: 936 sheet: 0.59 (0.25), residues: 432 loop : -1.96 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 184 TYR 0.023 0.001 TYR C 305 PHE 0.009 0.001 PHE B 184 TRP 0.011 0.001 TRP B 147 HIS 0.006 0.001 HIS B 114 Details of bonding type rmsd covalent geometry : bond 0.00225 (22729) covalent geometry : angle 0.51007 (30922) hydrogen bonds : bond 0.02784 ( 897) hydrogen bonds : angle 3.92692 ( 2592) Misc. bond : bond 0.00059 ( 1) =============================================================================== Job complete usr+sys time: 6678.40 seconds wall clock time: 114 minutes 30.51 seconds (6870.51 seconds total)