Starting phenix.real_space_refine on Thu Sep 18 23:57:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6b45_7049/09_2025/6b45_7049.cif Found real_map, /net/cci-nas-00/data/ceres_data/6b45_7049/09_2025/6b45_7049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6b45_7049/09_2025/6b45_7049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6b45_7049/09_2025/6b45_7049.map" model { file = "/net/cci-nas-00/data/ceres_data/6b45_7049/09_2025/6b45_7049.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6b45_7049/09_2025/6b45_7049.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 0.714 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 17 5.16 5 C 13067 2.51 5 N 4065 2.21 5 O 4339 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21547 Number of models: 1 Model: "" Number of chains: 10 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: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2566 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 322} 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: 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: "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': 10, 'rna2p_pyr': 11, 'rna3p_pur': 19, 'rna3p_pyr': 19} Link IDs: {'rna2p': 20, 'rna3p': 39} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 4.89, per 1000 atoms: 0.23 Number of scatterers: 21547 At special positions: 0 Unit cell: (158.76, 121.8, 150.36, 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 17 16.00 P 59 15.00 O 4339 8.00 N 4065 7.00 C 13067 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 961.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4386 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 30 sheets defined 26.8% alpha, 12.4% beta 1 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 Processing helix chain 'A' and resid 35 through 45 Processing helix chain 'A' and resid 51 through 60 removed outlier: 3.553A pdb=" N ASP A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.586A pdb=" N ILE A 73 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS A 74 " --> pdb=" O LYS A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 74' Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 148 through 161 removed outlier: 3.674A pdb=" N ALA A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 211 removed outlier: 3.864A pdb=" N PHE A 211 " --> pdb=" O ARG A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 Processing helix chain 'A' and resid 294 through 306 Processing helix chain 'A' and resid 322 through 341 Processing helix chain 'A' and resid 354 through 360 removed outlier: 4.090A pdb=" N ALA A 358 " --> pdb=" O GLN A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 399 removed outlier: 3.715A pdb=" N ASN A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 429 removed outlier: 4.017A pdb=" N SER A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' Processing helix chain 'B' and resid 33 through 53 removed outlier: 3.924A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N SER B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 removed outlier: 3.899A pdb=" N GLY B 135 " --> pdb=" O GLN B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 152 removed outlier: 3.583A pdb=" N PHE B 152 " --> pdb=" O ASN B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 178 removed outlier: 3.619A pdb=" N ARG B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 200 removed outlier: 3.643A pdb=" N LEU B 200 " --> pdb=" O HIS B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 214 removed outlier: 3.761A pdb=" N LEU B 214 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 295 removed outlier: 3.945A pdb=" N VAL B 295 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.999A pdb=" N LEU B 301 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 129 removed outlier: 4.024A pdb=" N GLN C 120 " --> pdb=" O ASP C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 144 Processing helix chain 'C' and resid 191 through 205 removed outlier: 4.244A pdb=" N LEU C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 263 removed outlier: 3.737A pdb=" N ALA C 263 " --> pdb=" O LYS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 313 removed outlier: 4.250A pdb=" N ASP C 309 " --> pdb=" O TYR C 305 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASN C 310 " --> pdb=" O THR C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 329 removed outlier: 4.711A pdb=" N TYR C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 36 removed outlier: 3.736A pdb=" N SER D 36 " --> pdb=" O ARG D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 68 removed outlier: 4.384A pdb=" N LEU D 67 " --> pdb=" O ASP D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 129 removed outlier: 3.876A pdb=" N GLN D 120 " --> pdb=" O ASP D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 144 removed outlier: 3.633A pdb=" N ASN D 141 " --> pdb=" O ARG D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 204 Processing helix chain 'D' and resid 256 through 263 removed outlier: 3.844A pdb=" N ALA D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 313 removed outlier: 4.281A pdb=" N ASP D 309 " --> pdb=" O TYR D 305 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU D 313 " --> pdb=" O ASP D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 332 removed outlier: 4.702A pdb=" N LEU D 330 " --> pdb=" O VAL D 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 70 Processing helix chain 'E' and resid 111 through 129 removed outlier: 3.554A pdb=" N ASP E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLN E 120 " --> pdb=" O ASP E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 144 removed outlier: 3.667A pdb=" N ARG E 137 " --> pdb=" O GLU E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 203 removed outlier: 4.069A pdb=" N LEU E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 263 Processing helix chain 'E' and resid 303 through 313 removed outlier: 4.531A pdb=" N ASP E 309 " --> pdb=" O TYR E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 333 removed outlier: 4.373A pdb=" N HIS E 324 " --> pdb=" O VAL E 320 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL E 326 " --> pdb=" O GLN E 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 36 removed outlier: 3.624A pdb=" N SER F 36 " --> pdb=" O ARG F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 129 removed outlier: 3.690A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN F 120 " --> pdb=" O ASP F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 144 Processing helix chain 'F' and resid 191 through 205 removed outlier: 3.677A pdb=" N LEU F 195 " --> pdb=" O GLU F 191 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY F 205 " --> pdb=" O SER F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 Processing helix chain 'F' and resid 303 through 313 removed outlier: 3.894A pdb=" N ASP F 309 " --> pdb=" O TYR F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 333 removed outlier: 3.946A pdb=" N VAL F 326 " --> pdb=" O GLN F 322 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY F 333 " --> pdb=" O ASN F 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 36 Processing helix chain 'G' and resid 66 through 71 Processing helix chain 'G' and resid 111 through 129 removed outlier: 3.876A pdb=" N ARG G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP G 116 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS G 117 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 140 Processing helix chain 'G' and resid 191 through 205 removed outlier: 3.676A pdb=" N LEU G 195 " --> pdb=" O GLU G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 263 Processing helix chain 'G' and resid 303 through 308 removed outlier: 3.723A pdb=" N LEU G 307 " --> pdb=" O ASP G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 333 removed outlier: 4.138A pdb=" N VAL G 326 " --> pdb=" O GLN G 322 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE G 327 " --> pdb=" O GLN G 323 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 36 removed outlier: 3.770A pdb=" N ALA H 35 " --> pdb=" O GLN H 32 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER H 36 " --> pdb=" O ARG H 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 32 through 36' Processing helix chain 'H' and resid 65 through 72 removed outlier: 3.639A pdb=" N GLN H 72 " --> pdb=" O ASP H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 129 removed outlier: 3.779A pdb=" N GLN H 120 " --> pdb=" O ASP H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 140 Processing helix chain 'H' and resid 192 through 204 Processing helix chain 'H' and resid 256 through 263 Processing helix chain 'H' and resid 303 through 313 removed outlier: 3.529A pdb=" N LEU H 307 " --> pdb=" O ASP H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 333 removed outlier: 4.320A pdb=" N HIS H 324 " --> pdb=" O VAL H 320 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N TYR H 325 " --> pdb=" O GLU H 321 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL H 326 " --> pdb=" O GLN H 322 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE H 327 " --> pdb=" O GLN H 323 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 32 removed outlier: 4.320A pdb=" N LEU L 20 " --> pdb=" O PRO L 16 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 77 removed outlier: 4.137A pdb=" N LEU L 76 " --> pdb=" O ARG L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 119 Processing helix chain 'L' and resid 123 through 130 removed outlier: 4.126A pdb=" N ALA L 127 " --> pdb=" O SER L 123 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 69 removed outlier: 3.752A pdb=" N THR A 69 " --> pdb=" O PHE A 194 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181 removed outlier: 3.602A pdb=" N PHE A 180 " --> pdb=" O HIS A 188 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS A 188 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ARG B 278 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU A 189 " --> pdb=" O ARG B 278 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL B 280 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 178 through 181 removed outlier: 3.602A pdb=" N PHE A 180 " --> pdb=" O HIS A 188 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS A 188 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ARG B 278 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU A 189 " --> pdb=" O ARG B 278 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL B 280 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 239 through 241 removed outlier: 3.544A pdb=" N ASN A 262 " --> pdb=" O GLN A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 15 through 16 removed outlier: 3.527A pdb=" N VAL B 107 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS B 104 " --> pdb=" O GLU B 67 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU B 67 " --> pdb=" O HIS B 104 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA7, first strand: chain 'C' and resid 19 through 20 removed outlier: 3.532A pdb=" N ARG C 98 " --> pdb=" O ASP C 19 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N VAL C 93 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ALA C 215 " --> pdb=" O VAL C 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 24 through 28 removed outlier: 4.905A pdb=" N VAL C 93 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ALA C 215 " --> pdb=" O VAL C 93 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 266 through 268 removed outlier: 5.060A pdb=" N ILE C 280 " --> pdb=" O ILE C 267 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.941A pdb=" N LEU D 12 " --> pdb=" O PHE D 336 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.795A pdb=" N ARG D 98 " --> pdb=" O ASP D 19 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA D 217 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL D 99 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL D 209 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU D 210 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA D 157 " --> pdb=" O ARG D 218 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.795A pdb=" N ARG D 98 " --> pdb=" O ASP D 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE D 255 " --> pdb=" O ALA D 23 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 45 through 49 removed outlier: 3.713A pdb=" N VAL D 49 " --> pdb=" O GLN D 77 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA D 82 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 287 through 288 Processing sheet with id=AB6, 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: 3.556A pdb=" N LEU E 24 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 19 through 20 removed outlier: 3.638A pdb=" N GLU E 212 " --> pdb=" O ASN E 163 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 45 through 49 removed outlier: 3.558A pdb=" N GLN E 77 " --> pdb=" O VAL E 49 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 248 through 249 Processing sheet with id=AC1, first strand: chain 'E' and resid 266 through 268 removed outlier: 5.257A pdb=" N ILE E 280 " --> pdb=" O ILE E 267 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 11 through 13 removed outlier: 3.605A pdb=" N LEU F 12 " --> pdb=" O PHE F 336 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 170 through 175 removed outlier: 4.384A pdb=" N ARG F 172 " --> pdb=" O HIS F 164 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU F 159 " --> pdb=" O PHE F 216 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE F 216 " --> pdb=" O GLU F 159 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU F 210 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL F 209 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL F 99 " --> pdb=" O VAL F 209 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ALA F 253 " --> pdb=" O MET F 25 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 45 through 51 removed outlier: 3.526A pdb=" N VAL F 49 " --> pdb=" O GLN F 77 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY F 51 " --> pdb=" O ASN F 75 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN F 75 " --> pdb=" O GLY F 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 12 through 13 Processing sheet with id=AC6, first strand: chain 'G' and resid 18 through 20 removed outlier: 4.290A pdb=" N VAL G 209 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU G 210 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU G 212 " --> pdb=" O ASN G 163 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN G 163 " --> pdb=" O GLU G 212 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU G 159 " --> pdb=" O PHE G 216 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 18 through 20 removed outlier: 3.783A pdb=" N ARG G 94 " --> pdb=" O LEU G 24 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU G 24 " --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ALA G 253 " --> pdb=" O MET G 25 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA G 252 " --> pdb=" O VAL G 249 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 45 through 50 removed outlier: 8.232A pdb=" N SER G 243 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N THR G 78 " --> pdb=" O SER G 243 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 12 through 13 removed outlier: 3.921A pdb=" N LEU H 12 " --> pdb=" O PHE H 336 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 24 through 26 removed outlier: 3.575A pdb=" N VAL H 99 " --> pdb=" O VAL H 209 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL H 209 " --> pdb=" O VAL H 99 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU H 210 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU H 212 " --> pdb=" O ASN H 163 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL H 160 " --> pdb=" O ARG H 175 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ARG H 175 " --> pdb=" O VAL H 160 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE H 162 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ALA H 173 " --> pdb=" O ILE H 162 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N HIS H 164 " --> pdb=" O ALA H 171 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 45 through 46 removed outlier: 3.611A pdb=" N VAL H 81 " --> pdb=" O ARG H 45 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 49 through 50 623 hydrogen bonds defined for protein. 1737 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3 hydrogen bonds 6 hydrogen bond angles 0 basepair planarities 1 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 3.11 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6363 1.33 - 1.45: 4315 1.45 - 1.58: 11233 1.58 - 1.70: 118 1.70 - 1.82: 25 Bond restraints: 22054 Sorted by residual: bond pdb=" C LEU B 181 " pdb=" N PRO B 182 " ideal model delta sigma weight residual 1.334 1.380 -0.046 8.40e-03 1.42e+04 2.99e+01 bond pdb=" C ASP G 63 " pdb=" N PRO G 64 " ideal model delta sigma weight residual 1.334 1.355 -0.022 8.40e-03 1.42e+04 6.77e+00 bond pdb=" CB ASN C 262 " pdb=" CG ASN C 262 " ideal model delta sigma weight residual 1.516 1.470 0.046 2.50e-02 1.60e+03 3.37e+00 bond pdb=" N VAL H 225 " pdb=" CA VAL H 225 " ideal model delta sigma weight residual 1.459 1.439 0.020 1.25e-02 6.40e+03 2.54e+00 bond pdb=" CG1 ILE F 260 " pdb=" CD1 ILE F 260 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.42e+00 ... (remaining 22049 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 29319 2.93 - 5.86: 596 5.86 - 8.79: 73 8.79 - 11.72: 18 11.72 - 14.65: 4 Bond angle restraints: 30010 Sorted by residual: angle pdb=" N ILE D 327 " pdb=" CA ILE D 327 " pdb=" C ILE D 327 " ideal model delta sigma weight residual 113.53 104.84 8.69 9.80e-01 1.04e+00 7.87e+01 angle pdb=" N LYS F 60 " pdb=" CA LYS F 60 " pdb=" C LYS F 60 " ideal model delta sigma weight residual 114.31 106.67 7.64 1.29e+00 6.01e-01 3.51e+01 angle pdb=" C ALA G 319 " pdb=" N VAL G 320 " pdb=" CA VAL G 320 " ideal model delta sigma weight residual 121.97 131.57 -9.60 1.80e+00 3.09e-01 2.85e+01 angle pdb=" C ARG E 250 " pdb=" N ASP E 251 " pdb=" CA ASP E 251 " ideal model delta sigma weight residual 121.54 131.48 -9.94 1.91e+00 2.74e-01 2.71e+01 angle pdb=" N VAL E 249 " pdb=" CA VAL E 249 " pdb=" C VAL E 249 " ideal model delta sigma weight residual 109.34 98.62 10.72 2.08e+00 2.31e-01 2.65e+01 ... (remaining 30005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.94: 12125 29.94 - 59.88: 385 59.88 - 89.81: 83 89.81 - 119.75: 7 119.75 - 149.69: 2 Dihedral angle restraints: 12602 sinusoidal: 5288 harmonic: 7314 Sorted by residual: 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 50.31 149.69 1 1.50e+01 4.44e-03 7.95e+01 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 52.71 147.29 1 1.50e+01 4.44e-03 7.86e+01 dihedral pdb=" CA SER A 227 " pdb=" C SER A 227 " pdb=" N TRP A 228 " pdb=" CA TRP A 228 " ideal model delta harmonic sigma weight residual 180.00 138.75 41.25 0 5.00e+00 4.00e-02 6.81e+01 ... (remaining 12599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2663 0.081 - 0.162: 404 0.162 - 0.243: 41 0.243 - 0.324: 3 0.324 - 0.405: 3 Chirality restraints: 3114 Sorted by residual: chirality pdb=" CB ILE F 232 " pdb=" CA ILE F 232 " pdb=" CG1 ILE F 232 " pdb=" CG2 ILE F 232 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" C1' C M 1 " pdb=" O4' C M 1 " pdb=" C2' C M 1 " pdb=" N1 C M 1 " both_signs ideal model delta sigma weight residual False 2.46 2.06 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CB ILE F 165 " pdb=" CA ILE F 165 " pdb=" CG1 ILE F 165 " pdb=" CG2 ILE F 165 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 3111 not shown) Planarity restraints: 3899 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 324 " -0.026 2.00e-02 2.50e+03 3.27e-02 1.60e+01 pdb=" CG HIS C 324 " 0.070 2.00e-02 2.50e+03 pdb=" ND1 HIS C 324 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 HIS C 324 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 HIS C 324 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS C 324 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 152 " -0.050 5.00e-02 4.00e+02 7.48e-02 8.96e+00 pdb=" N PRO B 153 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 153 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 153 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 63 " 0.049 5.00e-02 4.00e+02 7.47e-02 8.94e+00 pdb=" N PRO G 64 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO G 64 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO G 64 " 0.042 5.00e-02 4.00e+02 ... (remaining 3896 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4171 2.77 - 3.30: 18783 3.30 - 3.84: 35286 3.84 - 4.37: 39895 4.37 - 4.90: 67913 Nonbonded interactions: 166048 Sorted by model distance: nonbonded pdb=" OG SER C 290 " pdb=" O ASP L 12 " model vdw 2.240 3.040 nonbonded pdb=" OG SER C 86 " pdb=" OD2 ASP C 221 " model vdw 2.258 3.040 nonbonded pdb=" OH TYR G 271 " pdb=" O GLY G 278 " model vdw 2.264 3.040 nonbonded pdb=" OE1 GLU C 230 " pdb=" OG SER D 48 " model vdw 2.303 3.040 nonbonded pdb=" OH TYR G 305 " pdb=" O SER H 54 " model vdw 2.304 3.040 ... (remaining 166043 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.310 Find NCS groups from input model: 0.300 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: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 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 : 0.006 0.061 22054 Z= 0.263 Angle : 1.046 14.649 30010 Z= 0.560 Chirality : 0.059 0.405 3114 Planarity : 0.006 0.075 3899 Dihedral : 14.876 149.689 8216 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.26 % Favored : 87.64 % Rotamer: Outliers : 0.65 % Allowed : 4.55 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.05 (0.12), residues: 2855 helix: -3.63 (0.11), residues: 768 sheet: -2.46 (0.25), residues: 361 loop : -3.59 (0.12), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 296 TYR 0.030 0.003 TYR E 138 PHE 0.043 0.004 PHE F 95 TRP 0.049 0.004 TRP E 311 HIS 0.041 0.003 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00563 (22054) covalent geometry : angle 1.04561 (30010) hydrogen bonds : bond 0.19638 ( 615) hydrogen bonds : angle 8.93538 ( 1743) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 335 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 GLN cc_start: 0.6893 (tp-100) cc_final: 0.5722 (pt0) REVERT: B 21 ASN cc_start: 0.7699 (t0) cc_final: 0.7193 (p0) REVERT: B 160 LEU cc_start: 0.5634 (mp) cc_final: 0.5189 (tt) REVERT: B 170 ARG cc_start: 0.6206 (mtt180) cc_final: 0.5669 (ptm160) REVERT: C 218 ARG cc_start: 0.4067 (mtp180) cc_final: 0.2981 (tmt170) REVERT: C 316 GLU cc_start: 0.6459 (mm-30) cc_final: 0.6091 (tm-30) REVERT: D 290 SER cc_start: 0.8031 (m) cc_final: 0.7335 (t) REVERT: F 58 LYS cc_start: 0.7334 (tttt) cc_final: 0.7113 (mmtt) REVERT: G 75 ASN cc_start: 0.6646 (p0) cc_final: 0.6432 (p0) REVERT: G 76 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7427 (tt) REVERT: H 271 TYR cc_start: 0.7058 (p90) cc_final: 0.6733 (p90) outliers start: 12 outliers final: 1 residues processed: 343 average time/residue: 0.1592 time to fit residues: 81.0954 Evaluate side-chains 197 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 195 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain G residue 76 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 20.0000 chunk 111 optimal weight: 0.4980 overall best weight: 4.4988 ------------------------------------------------------------------------------- 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 237 ASN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 HIS B 82 ASN B 114 HIS ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS C 141 ASN ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN D 164 HIS ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 322 GLN F 75 ASN F 223 GLN ** G 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 GLN ** G 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 HIS H 151 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.175567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.154980 restraints weight = 44217.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.157187 restraints weight = 24784.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.158591 restraints weight = 16326.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.159491 restraints weight = 12135.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.160074 restraints weight = 9891.273| |-----------------------------------------------------------------------------| r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22054 Z= 0.176 Angle : 0.686 9.836 30010 Z= 0.361 Chirality : 0.045 0.286 3114 Planarity : 0.005 0.068 3899 Dihedral : 15.944 147.491 4055 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 2.38 % Allowed : 10.46 % Favored : 87.16 % 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 aren not related in a simple way. whole: -4.06 (0.13), residues: 2855 helix: -2.35 (0.15), residues: 775 sheet: -1.96 (0.25), residues: 365 loop : -3.19 (0.13), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 33 TYR 0.021 0.002 TYR E 114 PHE 0.032 0.002 PHE E 226 TRP 0.024 0.002 TRP E 311 HIS 0.017 0.002 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00386 (22054) covalent geometry : angle 0.68633 (30010) hydrogen bonds : bond 0.04722 ( 615) hydrogen bonds : angle 6.36334 ( 1743) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 228 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LEU cc_start: 0.7304 (mt) cc_final: 0.6769 (tt) REVERT: A 241 GLN cc_start: 0.7009 (tp-100) cc_final: 0.5868 (pt0) REVERT: B 160 LEU cc_start: 0.5577 (mp) cc_final: 0.5289 (tt) REVERT: B 170 ARG cc_start: 0.6462 (mtt180) cc_final: 0.5672 (mmm160) REVERT: B 315 ARG cc_start: 0.6262 (mtt-85) cc_final: 0.5986 (mtt-85) REVERT: C 167 GLN cc_start: 0.4994 (OUTLIER) cc_final: 0.4290 (pm20) REVERT: C 218 ARG cc_start: 0.3967 (mtp180) cc_final: 0.2894 (tmt170) REVERT: C 316 GLU cc_start: 0.6222 (mm-30) cc_final: 0.5949 (tm-30) REVERT: D 290 SER cc_start: 0.7729 (m) cc_final: 0.7429 (m) REVERT: E 208 HIS cc_start: 0.5957 (t-90) cc_final: 0.5461 (t70) REVERT: G 76 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7529 (tt) REVERT: H 271 TYR cc_start: 0.7027 (p90) cc_final: 0.6760 (p90) outliers start: 44 outliers final: 26 residues processed: 260 average time/residue: 0.1444 time to fit residues: 58.0465 Evaluate side-chains 210 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 303 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 178 optimal weight: 10.0000 chunk 223 optimal weight: 0.3980 chunk 29 optimal weight: 50.0000 chunk 194 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 209 optimal weight: 10.0000 chunk 217 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 231 optimal weight: 6.9990 overall best weight: 5.0788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 ASN H 110 ASN H 140 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.174784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.153799 restraints weight = 44636.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.155701 restraints weight = 26230.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.157067 restraints weight = 18050.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.157872 restraints weight = 13786.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.158436 restraints weight = 11485.397| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22054 Z= 0.186 Angle : 0.685 10.402 30010 Z= 0.356 Chirality : 0.045 0.264 3114 Planarity : 0.005 0.063 3899 Dihedral : 15.784 148.551 4053 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.24 % Favored : 88.72 % Rotamer: Outliers : 3.95 % Allowed : 12.62 % Favored : 83.42 % 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 aren not related in a simple way. whole: -3.63 (0.14), residues: 2855 helix: -1.76 (0.17), residues: 779 sheet: -1.68 (0.26), residues: 347 loop : -3.03 (0.13), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 146 TYR 0.020 0.002 TYR E 114 PHE 0.025 0.002 PHE C 131 TRP 0.022 0.002 TRP E 311 HIS 0.015 0.002 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00414 (22054) covalent geometry : angle 0.68504 (30010) hydrogen bonds : bond 0.04476 ( 615) hydrogen bonds : angle 6.05751 ( 1743) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 188 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 LEU cc_start: 0.7281 (mt) cc_final: 0.6829 (tt) REVERT: A 241 GLN cc_start: 0.6834 (tp-100) cc_final: 0.5942 (pt0) REVERT: B 21 ASN cc_start: 0.7754 (t0) cc_final: 0.7196 (p0) REVERT: B 170 ARG cc_start: 0.6466 (mtt180) cc_final: 0.5890 (mmp80) REVERT: B 315 ARG cc_start: 0.6322 (mtt-85) cc_final: 0.6081 (mtt-85) REVERT: C 167 GLN cc_start: 0.5081 (OUTLIER) cc_final: 0.4485 (pm20) REVERT: C 218 ARG cc_start: 0.4004 (mtp180) cc_final: 0.2814 (tmt170) REVERT: C 267 ILE cc_start: 0.7166 (mm) cc_final: 0.6799 (mm) REVERT: D 208 HIS cc_start: 0.7166 (OUTLIER) cc_final: 0.6811 (p-80) REVERT: D 290 SER cc_start: 0.7661 (m) cc_final: 0.7387 (m) REVERT: E 208 HIS cc_start: 0.6123 (t-90) cc_final: 0.5705 (t-90) REVERT: F 58 LYS cc_start: 0.7193 (mmtt) cc_final: 0.6951 (tttp) REVERT: F 213 VAL cc_start: 0.8939 (OUTLIER) cc_final: 0.8733 (t) REVERT: G 15 GLU cc_start: 0.6706 (mp0) cc_final: 0.6446 (mt-10) REVERT: H 271 TYR cc_start: 0.7094 (p90) cc_final: 0.6875 (p90) outliers start: 73 outliers final: 43 residues processed: 247 average time/residue: 0.1429 time to fit residues: 55.8259 Evaluate side-chains 213 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 167 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 HIS Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 303 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 78 optimal weight: 20.0000 chunk 138 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 254 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 chunk 240 optimal weight: 20.0000 chunk 29 optimal weight: 50.0000 chunk 220 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 204 optimal weight: 10.0000 overall best weight: 9.3992 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN E 163 ASN ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 322 GLN G 262 ASN ** G 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.169380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.149136 restraints weight = 44985.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.150725 restraints weight = 28147.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.150762 restraints weight = 22604.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.151584 restraints weight = 17852.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.151945 restraints weight = 14777.879| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 22054 Z= 0.301 Angle : 0.826 10.845 30010 Z= 0.430 Chirality : 0.050 0.299 3114 Planarity : 0.006 0.064 3899 Dihedral : 16.084 146.734 4053 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 14.43 % Favored : 85.53 % Rotamer: Outliers : 5.25 % Allowed : 13.98 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.68 (0.14), residues: 2855 helix: -1.81 (0.17), residues: 766 sheet: -1.77 (0.26), residues: 377 loop : -3.06 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 175 TYR 0.022 0.003 TYR C 247 PHE 0.027 0.003 PHE E 226 TRP 0.026 0.003 TRP E 311 HIS 0.018 0.002 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00675 (22054) covalent geometry : angle 0.82643 (30010) hydrogen bonds : bond 0.05119 ( 615) hydrogen bonds : angle 6.53140 ( 1743) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 181 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7146 (mt0) REVERT: A 206 LEU cc_start: 0.7541 (mt) cc_final: 0.7050 (tt) REVERT: A 241 GLN cc_start: 0.7085 (tp-100) cc_final: 0.5874 (pt0) REVERT: B 46 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7013 (mtm-85) REVERT: B 160 LEU cc_start: 0.5880 (tt) cc_final: 0.4535 (mt) REVERT: B 170 ARG cc_start: 0.6827 (mtt180) cc_final: 0.6031 (mmp80) REVERT: B 315 ARG cc_start: 0.6547 (mtt-85) cc_final: 0.6294 (mtt-85) REVERT: C 267 ILE cc_start: 0.7567 (mm) cc_final: 0.7154 (mm) REVERT: D 208 HIS cc_start: 0.7434 (OUTLIER) cc_final: 0.7149 (p-80) REVERT: F 58 LYS cc_start: 0.7225 (mmtt) cc_final: 0.6931 (tttp) REVERT: F 234 ASP cc_start: 0.7520 (m-30) cc_final: 0.7017 (p0) REVERT: G 224 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7440 (tt0) outliers start: 97 outliers final: 64 residues processed: 264 average time/residue: 0.1408 time to fit residues: 59.1992 Evaluate side-chains 227 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 159 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 HIS Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 303 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 39 optimal weight: 0.0970 chunk 209 optimal weight: 6.9990 chunk 237 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 199 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- 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 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 ASN C 151 ASN ** C 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN D 120 GLN ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 262 ASN ** G 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.175701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.155333 restraints weight = 44648.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.156911 restraints weight = 28228.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.156913 restraints weight = 22373.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.157766 restraints weight = 18041.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.158109 restraints weight = 14934.506| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22054 Z= 0.133 Angle : 0.629 9.246 30010 Z= 0.327 Chirality : 0.043 0.258 3114 Planarity : 0.005 0.061 3899 Dihedral : 15.567 154.741 4053 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 3.68 % Allowed : 16.47 % Favored : 79.85 % 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 aren not related in a simple way. whole: -3.21 (0.15), residues: 2855 helix: -1.29 (0.18), residues: 784 sheet: -1.54 (0.26), residues: 378 loop : -2.83 (0.14), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 268 TYR 0.019 0.002 TYR E 114 PHE 0.023 0.002 PHE E 226 TRP 0.012 0.001 TRP A 263 HIS 0.011 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00294 (22054) covalent geometry : angle 0.62923 (30010) hydrogen bonds : bond 0.03882 ( 615) hydrogen bonds : angle 5.64122 ( 1743) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 199 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 LEU cc_start: 0.7492 (mt) cc_final: 0.7050 (tt) REVERT: A 241 GLN cc_start: 0.7226 (tp-100) cc_final: 0.6124 (pt0) REVERT: B 21 ASN cc_start: 0.7720 (t0) cc_final: 0.7181 (p0) REVERT: B 160 LEU cc_start: 0.5881 (tt) cc_final: 0.4557 (mp) REVERT: B 170 ARG cc_start: 0.6670 (mtt180) cc_final: 0.5911 (mmp80) REVERT: C 167 GLN cc_start: 0.5190 (OUTLIER) cc_final: 0.4270 (pm20) REVERT: C 218 ARG cc_start: 0.4244 (mtp180) cc_final: 0.2967 (tmt170) REVERT: C 267 ILE cc_start: 0.7389 (mm) cc_final: 0.6923 (mm) REVERT: D 37 GLN cc_start: 0.7429 (pm20) cc_final: 0.6687 (mm110) REVERT: D 195 LEU cc_start: 0.5920 (tt) cc_final: 0.4905 (tt) REVERT: D 290 SER cc_start: 0.7386 (m) cc_final: 0.7065 (m) REVERT: E 208 HIS cc_start: 0.6600 (t-90) cc_final: 0.5727 (t-90) REVERT: F 58 LYS cc_start: 0.7137 (mmtt) cc_final: 0.6890 (tttp) REVERT: G 224 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7660 (tt0) outliers start: 68 outliers final: 39 residues processed: 249 average time/residue: 0.1499 time to fit residues: 59.2424 Evaluate side-chains 214 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 324 HIS Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 245 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 41 optimal weight: 30.0000 chunk 260 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 200 optimal weight: 20.0000 chunk 142 optimal weight: 6.9990 chunk 229 optimal weight: 5.9990 chunk 263 optimal weight: 9.9990 chunk 246 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 286 optimal weight: 20.0000 chunk 213 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN D 120 GLN ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.172619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.151718 restraints weight = 44685.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.153570 restraints weight = 26515.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.154876 restraints weight = 18469.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.155661 restraints weight = 14209.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.156217 restraints weight = 11928.193| |-----------------------------------------------------------------------------| r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22054 Z= 0.198 Angle : 0.687 9.593 30010 Z= 0.358 Chirality : 0.045 0.285 3114 Planarity : 0.005 0.061 3899 Dihedral : 15.635 151.567 4053 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.57 % Favored : 87.39 % Rotamer: Outliers : 4.50 % Allowed : 16.74 % Favored : 78.76 % 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 aren not related in a simple way. whole: -3.14 (0.15), residues: 2855 helix: -1.23 (0.18), residues: 772 sheet: -1.53 (0.27), residues: 367 loop : -2.76 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 268 TYR 0.022 0.002 TYR E 114 PHE 0.026 0.002 PHE C 131 TRP 0.017 0.002 TRP A 263 HIS 0.014 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00443 (22054) covalent geometry : angle 0.68749 (30010) hydrogen bonds : bond 0.04230 ( 615) hydrogen bonds : angle 5.83335 ( 1743) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 182 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 206 LEU cc_start: 0.7217 (mt) cc_final: 0.6848 (tt) REVERT: A 238 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7439 (pp) REVERT: A 241 GLN cc_start: 0.7066 (tp-100) cc_final: 0.6087 (pt0) REVERT: B 21 ASN cc_start: 0.7782 (t0) cc_final: 0.7213 (p0) REVERT: B 170 ARG cc_start: 0.6546 (mtt180) cc_final: 0.6125 (mmp80) REVERT: C 167 GLN cc_start: 0.5165 (OUTLIER) cc_final: 0.4614 (pm20) REVERT: C 267 ILE cc_start: 0.7471 (mm) cc_final: 0.7036 (mm) REVERT: D 30 TRP cc_start: 0.7400 (m-10) cc_final: 0.7117 (m100) REVERT: D 37 GLN cc_start: 0.7438 (pm20) cc_final: 0.6718 (mm-40) REVERT: D 120 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6868 (tm-30) REVERT: D 159 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6718 (pt0) REVERT: D 195 LEU cc_start: 0.5966 (tt) cc_final: 0.5304 (tt) REVERT: D 290 SER cc_start: 0.7332 (OUTLIER) cc_final: 0.7015 (m) REVERT: E 208 HIS cc_start: 0.6656 (t-90) cc_final: 0.5817 (t-90) REVERT: G 224 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7616 (tt0) REVERT: H 277 LEU cc_start: 0.6809 (OUTLIER) cc_final: 0.6415 (tt) outliers start: 83 outliers final: 59 residues processed: 247 average time/residue: 0.1402 time to fit residues: 54.8848 Evaluate side-chains 235 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 169 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 HIS Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 290 SER Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 260 ILE Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 303 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 208 optimal weight: 7.9990 chunk 286 optimal weight: 10.0000 chunk 251 optimal weight: 9.9990 chunk 247 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 288 optimal weight: 40.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.175214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.154885 restraints weight = 44547.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.156672 restraints weight = 27397.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.156497 restraints weight = 22012.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.157365 restraints weight = 17734.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.157893 restraints weight = 14375.483| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22054 Z= 0.138 Angle : 0.626 9.877 30010 Z= 0.325 Chirality : 0.043 0.267 3114 Planarity : 0.004 0.060 3899 Dihedral : 15.457 153.595 4053 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 4.28 % Allowed : 17.17 % Favored : 78.55 % 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 aren not related in a simple way. whole: -2.92 (0.15), residues: 2855 helix: -0.94 (0.18), residues: 774 sheet: -1.40 (0.27), residues: 361 loop : -2.67 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 268 TYR 0.023 0.002 TYR E 114 PHE 0.023 0.002 PHE E 226 TRP 0.013 0.001 TRP A 263 HIS 0.012 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00307 (22054) covalent geometry : angle 0.62623 (30010) hydrogen bonds : bond 0.03817 ( 615) hydrogen bonds : angle 5.49558 ( 1743) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 183 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.6967 (mt0) REVERT: A 206 LEU cc_start: 0.7485 (mt) cc_final: 0.7070 (tt) REVERT: A 238 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7260 (pp) REVERT: A 241 GLN cc_start: 0.7211 (tp-100) cc_final: 0.6131 (pt0) REVERT: B 21 ASN cc_start: 0.7736 (t0) cc_final: 0.7190 (p0) REVERT: B 170 ARG cc_start: 0.6569 (mtt180) cc_final: 0.5981 (mmp80) REVERT: B 281 GLU cc_start: 0.6936 (tm-30) cc_final: 0.6663 (tt0) REVERT: C 167 GLN cc_start: 0.5252 (OUTLIER) cc_final: 0.4484 (pm20) REVERT: C 218 ARG cc_start: 0.4419 (mtp180) cc_final: 0.3072 (tmt170) REVERT: C 267 ILE cc_start: 0.7519 (mm) cc_final: 0.7013 (mm) REVERT: D 30 TRP cc_start: 0.7335 (m-10) cc_final: 0.7103 (m100) REVERT: D 37 GLN cc_start: 0.7405 (pm20) cc_final: 0.6728 (mm110) REVERT: D 120 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.6814 (pp30) REVERT: D 260 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8083 (tt) REVERT: D 290 SER cc_start: 0.7415 (OUTLIER) cc_final: 0.7099 (m) REVERT: E 208 HIS cc_start: 0.6577 (t-90) cc_final: 0.5728 (t-90) REVERT: G 224 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7671 (tt0) REVERT: H 277 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6459 (tt) outliers start: 79 outliers final: 51 residues processed: 244 average time/residue: 0.1537 time to fit residues: 59.1609 Evaluate side-chains 233 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 174 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 324 HIS Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 290 SER Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 303 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 271 optimal weight: 50.0000 chunk 225 optimal weight: 7.9990 chunk 227 optimal weight: 9.9990 chunk 163 optimal weight: 5.9990 chunk 286 optimal weight: 20.0000 chunk 231 optimal weight: 8.9990 chunk 185 optimal weight: 9.9990 chunk 196 optimal weight: 10.0000 chunk 251 optimal weight: 6.9990 chunk 14 optimal weight: 40.0000 chunk 69 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 GLN G 229 GLN ** G 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.170715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.150525 restraints weight = 44837.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.151959 restraints weight = 28090.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.151956 restraints weight = 23251.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.152906 restraints weight = 18304.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.153161 restraints weight = 14941.959| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 22054 Z= 0.245 Angle : 0.740 9.947 30010 Z= 0.384 Chirality : 0.047 0.290 3114 Planarity : 0.005 0.061 3899 Dihedral : 15.715 148.635 4053 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.94 % Favored : 86.02 % Rotamer: Outliers : 4.55 % Allowed : 17.55 % Favored : 77.90 % 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 aren not related in a simple way. whole: -3.11 (0.15), residues: 2855 helix: -1.16 (0.18), residues: 771 sheet: -1.51 (0.27), residues: 367 loop : -2.77 (0.14), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 146 TYR 0.022 0.002 TYR E 114 PHE 0.028 0.003 PHE C 131 TRP 0.023 0.002 TRP A 263 HIS 0.015 0.002 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00549 (22054) covalent geometry : angle 0.74013 (30010) hydrogen bonds : bond 0.04527 ( 615) hydrogen bonds : angle 5.98413 ( 1743) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 177 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.6977 (mt0) REVERT: A 206 LEU cc_start: 0.7401 (mt) cc_final: 0.6929 (tt) REVERT: A 238 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7344 (pp) REVERT: A 241 GLN cc_start: 0.7141 (tp-100) cc_final: 0.5994 (pt0) REVERT: B 170 ARG cc_start: 0.6630 (mtt180) cc_final: 0.6059 (mmp80) REVERT: C 167 GLN cc_start: 0.5113 (OUTLIER) cc_final: 0.4415 (pm20) REVERT: C 267 ILE cc_start: 0.7701 (mm) cc_final: 0.7314 (mm) REVERT: D 37 GLN cc_start: 0.7482 (pm20) cc_final: 0.6753 (mm110) REVERT: G 224 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7511 (tt0) outliers start: 84 outliers final: 68 residues processed: 245 average time/residue: 0.1400 time to fit residues: 54.9477 Evaluate side-chains 238 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 166 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 324 HIS Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 290 SER Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 303 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 240 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 200 optimal weight: 0.9990 chunk 186 optimal weight: 6.9990 chunk 211 optimal weight: 2.9990 chunk 156 optimal weight: 8.9990 chunk 246 optimal weight: 9.9990 chunk 4 optimal weight: 30.0000 chunk 113 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 86 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.173468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.153234 restraints weight = 44605.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.154606 restraints weight = 28131.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.154664 restraints weight = 22452.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.155679 restraints weight = 18787.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.155639 restraints weight = 15134.077| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22054 Z= 0.164 Angle : 0.661 11.313 30010 Z= 0.342 Chirality : 0.044 0.269 3114 Planarity : 0.005 0.060 3899 Dihedral : 15.520 150.053 4053 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 4.33 % Allowed : 17.88 % Favored : 77.79 % 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 aren not related in a simple way. whole: -2.95 (0.15), residues: 2855 helix: -1.00 (0.18), residues: 779 sheet: -1.47 (0.27), residues: 367 loop : -2.67 (0.14), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 268 TYR 0.022 0.002 TYR E 114 PHE 0.026 0.002 PHE E 226 TRP 0.017 0.002 TRP A 263 HIS 0.012 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00367 (22054) covalent geometry : angle 0.66128 (30010) hydrogen bonds : bond 0.03955 ( 615) hydrogen bonds : angle 5.63767 ( 1743) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 176 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.6861 (mt0) REVERT: A 206 LEU cc_start: 0.7522 (mt) cc_final: 0.7066 (tt) REVERT: A 238 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7285 (pp) REVERT: A 241 GLN cc_start: 0.7232 (tp-100) cc_final: 0.6078 (pt0) REVERT: B 11 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7959 (tt) REVERT: B 170 ARG cc_start: 0.6535 (mtt180) cc_final: 0.5941 (mmp80) REVERT: C 167 GLN cc_start: 0.5117 (OUTLIER) cc_final: 0.4507 (pm20) REVERT: C 218 ARG cc_start: 0.4549 (mtp180) cc_final: 0.3168 (tmt170) REVERT: C 267 ILE cc_start: 0.7580 (mm) cc_final: 0.7185 (mm) REVERT: D 30 TRP cc_start: 0.7390 (m-10) cc_final: 0.7097 (m100) REVERT: D 37 GLN cc_start: 0.7371 (pm20) cc_final: 0.6709 (mm110) REVERT: G 224 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7619 (tt0) outliers start: 80 outliers final: 63 residues processed: 239 average time/residue: 0.1496 time to fit residues: 56.9753 Evaluate side-chains 242 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 174 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 324 HIS Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 290 SER Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 303 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 172 optimal weight: 30.0000 chunk 240 optimal weight: 20.0000 chunk 228 optimal weight: 0.7980 chunk 68 optimal weight: 20.0000 chunk 37 optimal weight: 40.0000 chunk 43 optimal weight: 20.0000 chunk 177 optimal weight: 6.9990 chunk 207 optimal weight: 0.6980 chunk 248 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 12 optimal weight: 50.0000 overall best weight: 3.6986 ------------------------------------------------------------------------------- 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 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.174618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.153715 restraints weight = 44763.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.155692 restraints weight = 26448.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.156997 restraints weight = 18152.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.157757 restraints weight = 13956.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.158241 restraints weight = 11724.356| |-----------------------------------------------------------------------------| r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22054 Z= 0.150 Angle : 0.639 11.789 30010 Z= 0.329 Chirality : 0.043 0.250 3114 Planarity : 0.005 0.059 3899 Dihedral : 15.380 148.056 4053 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 3.79 % Allowed : 18.69 % Favored : 77.52 % 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 aren not related in a simple way. whole: -2.81 (0.15), residues: 2855 helix: -0.81 (0.18), residues: 774 sheet: -1.38 (0.27), residues: 363 loop : -2.62 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 146 TYR 0.023 0.002 TYR E 114 PHE 0.054 0.002 PHE C 95 TRP 0.017 0.001 TRP A 263 HIS 0.012 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00336 (22054) covalent geometry : angle 0.63895 (30010) hydrogen bonds : bond 0.03742 ( 615) hydrogen bonds : angle 5.43939 ( 1743) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 184 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.6901 (mt0) REVERT: A 206 LEU cc_start: 0.7349 (mt) cc_final: 0.6962 (tt) REVERT: A 241 GLN cc_start: 0.7320 (tp-100) cc_final: 0.6330 (pt0) REVERT: B 11 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8031 (tt) REVERT: B 170 ARG cc_start: 0.6396 (mtt180) cc_final: 0.6080 (mmp80) REVERT: B 315 ARG cc_start: 0.6354 (mtt-85) cc_final: 0.6046 (mtt-85) REVERT: C 167 GLN cc_start: 0.5079 (OUTLIER) cc_final: 0.4570 (pm20) REVERT: C 218 ARG cc_start: 0.4294 (mtp180) cc_final: 0.3045 (tmt170) REVERT: C 267 ILE cc_start: 0.7495 (mm) cc_final: 0.7086 (mm) REVERT: D 30 TRP cc_start: 0.7330 (m-10) cc_final: 0.7077 (m100) REVERT: D 37 GLN cc_start: 0.7361 (pm20) cc_final: 0.6745 (mm110) REVERT: G 224 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7699 (tt0) REVERT: H 181 ILE cc_start: 0.7460 (OUTLIER) cc_final: 0.7160 (tp) outliers start: 70 outliers final: 55 residues processed: 237 average time/residue: 0.1538 time to fit residues: 57.4120 Evaluate side-chains 230 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 170 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 324 HIS Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 290 SER Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 303 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 93 optimal weight: 6.9990 chunk 256 optimal weight: 30.0000 chunk 192 optimal weight: 1.9990 chunk 267 optimal weight: 20.0000 chunk 201 optimal weight: 4.9990 chunk 53 optimal weight: 30.0000 chunk 272 optimal weight: 30.0000 chunk 3 optimal weight: 40.0000 chunk 42 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 257 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.174292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.153891 restraints weight = 44891.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.155578 restraints weight = 28172.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.155498 restraints weight = 21993.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.156322 restraints weight = 18253.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.156717 restraints weight = 14893.360| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22054 Z= 0.157 Angle : 0.648 11.747 30010 Z= 0.333 Chirality : 0.043 0.260 3114 Planarity : 0.005 0.060 3899 Dihedral : 15.333 146.634 4053 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 3.85 % Allowed : 18.96 % Favored : 77.19 % 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 aren not related in a simple way. whole: -2.76 (0.15), residues: 2855 helix: -0.78 (0.18), residues: 780 sheet: -1.37 (0.28), residues: 363 loop : -2.57 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 268 TYR 0.023 0.002 TYR E 114 PHE 0.049 0.002 PHE C 95 TRP 0.019 0.001 TRP A 263 HIS 0.012 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00352 (22054) covalent geometry : angle 0.64780 (30010) hydrogen bonds : bond 0.03784 ( 615) hydrogen bonds : angle 5.43821 ( 1743) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3450.82 seconds wall clock time: 60 minutes 20.66 seconds (3620.66 seconds total)