Starting phenix.real_space_refine on Fri Sep 19 02:37:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6b44_7048/09_2025/6b44_7048.cif Found real_map, /net/cci-nas-00/data/ceres_data/6b44_7048/09_2025/6b44_7048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6b44_7048/09_2025/6b44_7048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6b44_7048/09_2025/6b44_7048.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6b44_7048/09_2025/6b44_7048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6b44_7048/09_2025/6b44_7048.map" } resolution = 2.9 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= 0.016 sd= 0.757 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 114 5.49 5 S 18 5.16 5 C 13604 2.51 5 N 4284 2.21 5 O 4661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s 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: 22681 Number of models: 1 Model: "" Number of chains: 12 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: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2569 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 761 Classifications: {'peptide': 189} Incomplete info: {'backbone_only': 173} Link IDs: {'PTRANS': 15, 'TRANS': 173} Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 803 Unresolved non-hydrogen angles: 1149 Unresolved non-hydrogen dihedrals: 531 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: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1276 Classifications: {'RNA': 60} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 13, 'rna3p_pur': 21, 'rna3p_pyr': 18} Link IDs: {'rna2p': 20, 'rna3p': 39} Chain: "N" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 850 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "O" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 262 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Time building chain proxies: 4.96, per 1000 atoms: 0.22 Number of scatterers: 22681 At special positions: 0 Unit cell: (133.715, 133.715, 182.413, 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 18 16.00 P 114 15.00 O 4661 8.00 N 4284 7.00 C 13604 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: 1.73 Conformation dependent library (CDL) restraints added in 997.6 milliseconds Enol-peptide restraints added in 953.7 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: 78 helices and 38 sheets defined 29.1% alpha, 16.4% beta 30 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 2.55 Creating SS restraints... Processing helix chain 'A' and resid 14 through 28 removed outlier: 3.548A pdb=" N GLU A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG A 24 " --> pdb=" O PHE A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 48 Processing helix chain 'A' and resid 51 through 59 Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.892A pdb=" N HIS A 74 " --> pdb=" O LYS A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.910A pdb=" N LEU A 115 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 123 removed outlier: 3.775A pdb=" N PHE A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 129 through 134 removed outlier: 4.498A pdb=" N ASN A 132 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU A 134 " --> pdb=" O LEU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 195 through 208 removed outlier: 3.711A pdb=" N GLU A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 removed outlier: 4.377A pdb=" N ARG A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 4.265A pdb=" N ASN A 250 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 317 through 320 removed outlier: 3.646A pdb=" N GLN A 320 " --> pdb=" O ALA A 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 317 through 320' Processing helix chain 'A' and resid 321 through 341 removed outlier: 3.961A pdb=" N VAL A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ALA A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU A 332 " --> pdb=" O GLN A 328 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 363 Processing helix chain 'A' and resid 386 through 399 removed outlier: 4.023A pdb=" N ARG A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A 398 " --> pdb=" O TRP A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 411 through 429 removed outlier: 5.072A pdb=" N GLU A 417 " --> pdb=" O GLN A 413 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU A 418 " --> pdb=" O TRP A 414 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N MET A 424 " --> pdb=" O LYS A 420 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU A 427 " --> pdb=" O THR A 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 46 removed outlier: 3.973A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 122 through 135 removed outlier: 3.917A pdb=" N ILE B 126 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 190 through 196 removed outlier: 3.756A pdb=" N GLN B 194 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 214 removed outlier: 3.710A pdb=" N LEU B 214 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 295 removed outlier: 3.616A pdb=" N VAL B 295 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'C' and resid 111 through 128 removed outlier: 3.592A pdb=" N ARG C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLN C 120 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP C 128 " --> pdb=" O THR C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 144 removed outlier: 3.853A pdb=" N ARG C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASN C 141 " --> pdb=" O ARG C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 204 removed outlier: 3.849A pdb=" N LEU C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER C 204 " --> pdb=" O ALA C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 264 removed outlier: 4.404A pdb=" N ILE C 260 " --> pdb=" O HIS C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 313 removed outlier: 4.352A pdb=" N ASP C 309 " --> pdb=" O TYR C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 333 Processing helix chain 'D' and resid 111 through 127 removed outlier: 3.705A pdb=" N GLN D 120 " --> pdb=" O ASP D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 144 Processing helix chain 'D' and resid 189 through 204 removed outlier: 3.507A pdb=" N LEU D 198 " --> pdb=" O ALA D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 265 removed outlier: 3.839A pdb=" N ILE D 260 " --> pdb=" O HIS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 312 removed outlier: 4.601A pdb=" N ASP D 309 " --> pdb=" O TYR D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 333 Processing helix chain 'E' and resid 67 through 72 removed outlier: 3.657A pdb=" N GLN E 72 " --> pdb=" O ASP E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 129 removed outlier: 3.906A pdb=" N GLN E 120 " --> pdb=" O ASP E 116 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN E 129 " --> pdb=" O TYR E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 144 removed outlier: 3.586A pdb=" N ARG E 137 " --> pdb=" O GLU E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 204 removed outlier: 3.633A pdb=" N LEU E 195 " --> pdb=" O GLU E 191 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 264 Processing helix chain 'E' and resid 274 through 278 removed outlier: 3.993A pdb=" N LEU E 277 " --> pdb=" O GLU E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 287 removed outlier: 4.231A pdb=" N SER E 287 " --> pdb=" O PRO E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 313 removed outlier: 4.084A pdb=" N ASP E 309 " --> pdb=" O TYR E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 333 removed outlier: 3.566A pdb=" N TYR E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 36 Processing helix chain 'F' and resid 65 through 73 Processing helix chain 'F' and resid 111 through 129 removed outlier: 3.606A pdb=" N ASN F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP F 128 " --> pdb=" O THR F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 144 removed outlier: 3.670A pdb=" N ARG F 137 " --> pdb=" O GLU F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 204 removed outlier: 3.954A pdb=" N LEU F 195 " --> pdb=" O GLU F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 Processing helix chain 'F' and resid 303 through 313 removed outlier: 4.002A pdb=" N ASP F 309 " --> pdb=" O TYR F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 333 removed outlier: 3.860A pdb=" N HIS F 324 " --> pdb=" O VAL F 320 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 39 removed outlier: 4.422A pdb=" N GLU G 38 " --> pdb=" O ALA G 35 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TRP G 39 " --> pdb=" O SER G 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 35 through 39' Processing helix chain 'G' and resid 66 through 71 removed outlier: 3.839A pdb=" N ILE G 71 " --> pdb=" O LEU G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 127 Processing helix chain 'G' and resid 131 through 144 removed outlier: 3.622A pdb=" N ARG G 137 " --> pdb=" O GLU G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 204 removed outlier: 3.747A pdb=" N ASP G 193 " --> pdb=" O ASP G 189 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA G 194 " --> pdb=" O ALA G 190 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU G 195 " --> pdb=" O GLU G 191 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU G 198 " --> pdb=" O ALA G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 265 removed outlier: 3.558A pdb=" N ILE G 260 " --> pdb=" O HIS G 256 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG G 265 " --> pdb=" O GLY G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 313 removed outlier: 4.530A pdb=" N ASP G 309 " --> pdb=" O TYR G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 333 removed outlier: 3.836A pdb=" N TYR G 325 " --> pdb=" O GLU G 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 39 removed outlier: 4.274A pdb=" N GLU H 38 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TRP H 39 " --> pdb=" O SER H 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 35 through 39' Processing helix chain 'H' and resid 58 through 62 removed outlier: 4.032A pdb=" N ASP H 61 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG H 62 " --> pdb=" O THR H 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 58 through 62' Processing helix chain 'H' and resid 111 through 129 removed outlier: 3.644A pdb=" N GLN H 120 " --> pdb=" O ASP H 116 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP H 128 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN H 129 " --> pdb=" O TYR H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 144 removed outlier: 4.065A pdb=" N ARG H 137 " --> pdb=" O GLU H 133 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN H 141 " --> pdb=" O ARG H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 204 removed outlier: 4.202A pdb=" N ALA H 194 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LEU H 195 " --> pdb=" O GLU H 191 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU H 198 " --> pdb=" O ALA H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 265 Processing helix chain 'H' and resid 303 through 313 Processing helix chain 'H' and resid 319 through 333 removed outlier: 3.513A pdb=" N TYR H 325 " --> pdb=" O GLU H 321 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU H 330 " --> pdb=" O VAL H 326 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 30 removed outlier: 4.813A pdb=" N VAL L 23 " --> pdb=" O GLN L 19 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N HIS L 29 " --> pdb=" O PHE L 25 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLN L 30 " --> pdb=" O GLY L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 77 removed outlier: 4.055A pdb=" N LEU L 76 " --> pdb=" O ARG L 73 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU L 77 " --> pdb=" O PRO L 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 73 through 77' Processing helix chain 'L' and resid 78 through 82 removed outlier: 4.240A pdb=" N ASP L 81 " --> pdb=" O GLY L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 120 removed outlier: 4.429A pdb=" N ARG L 118 " --> pdb=" O ARG L 114 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 removed outlier: 3.744A pdb=" N ASP A 107 " --> pdb=" O VAL A 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181 removed outlier: 8.376A pdb=" N ARG B 278 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU A 189 " --> pdb=" O ARG B 278 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL B 280 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N PHE B 279 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ALA B 257 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 234 removed outlier: 3.633A pdb=" N PHE A 232 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE B 219 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU A 234 " --> pdb=" O CYS B 217 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS B 217 " --> pdb=" O GLU A 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 239 through 241 removed outlier: 3.576A pdb=" N GLN A 241 " --> pdb=" O ASN A 262 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN A 262 " --> pdb=" O GLN A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 65 through 68 removed outlier: 3.519A pdb=" N ARG B 65 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU B 106 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ALA B 103 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLN B 18 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU B 105 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N SER B 16 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL B 107 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ARG B 14 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 159 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA B 157 " --> pdb=" O LEU B 11 " (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 'B' and resid 185 through 188 removed outlier: 3.571A pdb=" N VAL B 187 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU B 288 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 304 through 305 Processing sheet with id=AA9, first strand: chain 'C' and resid 23 through 25 removed outlier: 4.198A pdb=" N ALA C 253 " --> pdb=" O MET C 25 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 46 through 47 removed outlier: 4.205A pdb=" N VAL C 79 " --> pdb=" O LYS C 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 95 through 96 removed outlier: 3.676A pdb=" N VAL C 214 " --> pdb=" O ARG C 161 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG C 161 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE C 216 " --> pdb=" O GLU C 159 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLU C 159 " --> pdb=" O PHE C 216 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG C 172 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 95 through 96 removed outlier: 3.676A pdb=" N VAL C 214 " --> pdb=" O ARG C 161 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG C 161 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE C 216 " --> pdb=" O GLU C 159 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLU C 159 " --> pdb=" O PHE C 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 19 through 20 removed outlier: 4.223A pdb=" N VAL D 209 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU D 210 " --> pdb=" O ILE D 165 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 170 through 172 removed outlier: 6.484A pdb=" N HIS D 164 " --> pdb=" O ALA D 171 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU D 210 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL D 209 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET D 25 " --> pdb=" O ALA D 253 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ALA D 253 " --> pdb=" O MET D 25 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D 249 " --> pdb=" O ALA D 252 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 287 through 288 removed outlier: 4.260A pdb=" N VAL D 288 " --> pdb=" O LYS D 293 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS D 293 " --> pdb=" O VAL D 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 19 through 20 removed outlier: 3.523A pdb=" N VAL E 99 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL E 209 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU E 210 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL E 158 " --> pdb=" O ASP E 177 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ASP E 177 " --> pdb=" O VAL E 158 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL E 160 " --> pdb=" O ARG E 175 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ARG E 175 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE E 162 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA E 173 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N HIS E 164 " --> pdb=" O ALA E 171 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 19 through 20 removed outlier: 3.533A pdb=" N ILE E 255 " --> pdb=" O ALA E 23 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 44 through 52 removed outlier: 4.619A pdb=" N ALA E 82 " --> pdb=" O VAL E 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 108 through 109 removed outlier: 3.837A pdb=" N ALA F 108 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY F 334 " --> pdb=" O PHE F 14 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 19 through 20 removed outlier: 4.449A pdb=" N VAL F 209 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU F 210 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA F 157 " --> pdb=" O ARG F 218 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG F 172 " --> pdb=" O HIS F 164 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 19 through 20 removed outlier: 5.066A pdb=" N ALA F 253 " --> pdb=" O MET F 25 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 252 " --> pdb=" O VAL F 249 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 44 through 51 Processing sheet with id=AC5, first strand: chain 'F' and resid 266 through 268 Processing sheet with id=AC6, first strand: chain 'F' and resid 287 through 288 removed outlier: 3.525A pdb=" N LYS F 293 " --> pdb=" O VAL F 288 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 13 through 14 Processing sheet with id=AC8, first strand: chain 'G' and resid 19 through 20 removed outlier: 4.424A pdb=" N VAL G 209 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LEU G 210 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA G 157 " --> pdb=" O ARG G 218 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL G 160 " --> pdb=" O ARG G 175 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG G 175 " --> pdb=" O VAL G 160 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE G 162 " --> pdb=" O ALA G 173 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ALA G 173 " --> pdb=" O ILE G 162 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N HIS G 164 " --> pdb=" O ALA G 171 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 19 through 20 removed outlier: 4.791A pdb=" N ALA G 253 " --> pdb=" O MET G 25 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA G 252 " --> pdb=" O VAL G 249 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 45 through 52 removed outlier: 3.790A pdb=" N ASN G 75 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA G 82 " --> pdb=" O VAL G 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 266 through 268 Processing sheet with id=AD3, first strand: chain 'G' and resid 287 through 288 Processing sheet with id=AD4, first strand: chain 'H' and resid 108 through 109 removed outlier: 3.538A pdb=" N ALA H 108 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU H 12 " --> pdb=" O PHE H 336 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.933A pdb=" N LEU H 210 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA H 157 " --> pdb=" O ARG H 218 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL H 158 " --> pdb=" O ASP H 177 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ASP H 177 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL H 160 " --> pdb=" O ARG H 175 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG H 175 " --> pdb=" O VAL H 160 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE H 162 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ALA H 173 " --> pdb=" O ILE H 162 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N HIS H 164 " --> pdb=" O ALA H 171 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.527A pdb=" N ILE H 255 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ALA H 253 " --> pdb=" O MET H 25 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 45 through 52 removed outlier: 4.429A pdb=" N ALA H 82 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 266 through 268 Processing sheet with id=AD9, first strand: chain 'H' and resid 287 through 288 removed outlier: 3.528A pdb=" N LYS H 293 " --> pdb=" O VAL H 288 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 4 through 5 removed outlier: 4.190A pdb=" N TYR L 4 " --> pdb=" O ALA L 89 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 41 through 42 removed outlier: 3.543A pdb=" N HIS L 61 " --> pdb=" O GLY L 41 " (cutoff:3.500A) 721 hydrogen bonds defined for protein. 1989 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 75 hydrogen bonds 146 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 3.89 Time building geometry restraints manager: 2.21 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: 6685 1.33 - 1.46: 5321 1.46 - 1.58: 11067 1.58 - 1.70: 225 1.70 - 1.82: 27 Bond restraints: 23325 Sorted by residual: bond pdb=" C PHE B 152 " pdb=" N PRO B 153 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.41e+00 bond pdb=" CB THR G 289 " pdb=" CG2 THR G 289 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.37e+00 bond pdb=" CG1 ILE E 260 " pdb=" CD1 ILE E 260 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.34e+00 bond pdb=" C TRP C 39 " pdb=" N PRO C 40 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.87e+00 bond pdb=" CB ILE C 327 " pdb=" CG2 ILE C 327 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.74e+00 ... (remaining 23320 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 31566 3.43 - 6.85: 352 6.85 - 10.28: 31 10.28 - 13.71: 6 13.71 - 17.14: 2 Bond angle restraints: 31957 Sorted by residual: angle pdb=" C ARG D 250 " pdb=" N ASP D 251 " pdb=" CA ASP D 251 " ideal model delta sigma weight residual 121.54 132.02 -10.48 1.91e+00 2.74e-01 3.01e+01 angle pdb=" N ILE E 267 " pdb=" CA ILE E 267 " pdb=" C ILE E 267 " ideal model delta sigma weight residual 112.96 107.51 5.45 1.00e+00 1.00e+00 2.97e+01 angle pdb=" C ARG F 250 " pdb=" N ASP F 251 " pdb=" CA ASP F 251 " ideal model delta sigma weight residual 121.54 131.34 -9.80 1.91e+00 2.74e-01 2.63e+01 angle pdb=" N VAL F 249 " pdb=" CA VAL F 249 " pdb=" C VAL F 249 " ideal model delta sigma weight residual 109.34 98.77 10.57 2.08e+00 2.31e-01 2.58e+01 angle pdb=" C ARG G 250 " pdb=" N ASP G 251 " pdb=" CA ASP G 251 " ideal model delta sigma weight residual 122.46 129.62 -7.16 1.41e+00 5.03e-01 2.58e+01 ... (remaining 31952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 12709 35.22 - 70.43: 466 70.43 - 105.65: 38 105.65 - 140.86: 1 140.86 - 176.08: 3 Dihedral angle restraints: 13217 sinusoidal: 5903 harmonic: 7314 Sorted by residual: dihedral pdb=" O4' C M 1 " pdb=" C1' C M 1 " pdb=" N1 C M 1 " pdb=" C2 C M 1 " ideal model delta sinusoidal sigma weight residual 200.00 48.43 151.57 1 1.50e+01 4.44e-03 8.02e+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 51.46 148.54 1 1.50e+01 4.44e-03 7.91e+01 dihedral pdb=" O4' C M 20 " pdb=" C1' C M 20 " pdb=" N1 C M 20 " pdb=" C2 C M 20 " ideal model delta sinusoidal sigma weight residual 232.00 55.92 176.08 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 13214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2347 0.056 - 0.112: 785 0.112 - 0.168: 170 0.168 - 0.224: 20 0.224 - 0.280: 9 Chirality restraints: 3331 Sorted by residual: chirality pdb=" CB VAL B 322 " pdb=" CA VAL B 322 " pdb=" CG1 VAL B 322 " pdb=" CG2 VAL B 322 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C1' C M 16 " pdb=" O4' C M 16 " pdb=" C2' C M 16 " pdb=" N1 C M 16 " both_signs ideal model delta sigma weight residual False 2.47 2.20 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA ASN A 237 " pdb=" N ASN A 237 " pdb=" C ASN A 237 " pdb=" CB ASN A 237 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 3328 not shown) Planarity restraints: 3954 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 311 " 0.031 2.00e-02 2.50e+03 2.48e-02 1.53e+01 pdb=" CG TRP D 311 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP D 311 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP D 311 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP D 311 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 311 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 311 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 311 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 311 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP D 311 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 311 " 0.027 2.00e-02 2.50e+03 2.24e-02 1.25e+01 pdb=" CG TRP E 311 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP E 311 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP E 311 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 311 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 311 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 311 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 311 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 311 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP E 311 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 311 " 0.030 2.00e-02 2.50e+03 2.16e-02 1.17e+01 pdb=" CG TRP F 311 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP F 311 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP F 311 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP F 311 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP F 311 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP F 311 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 311 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 311 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 311 " 0.005 2.00e-02 2.50e+03 ... (remaining 3951 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4130 2.77 - 3.30: 19156 3.30 - 3.83: 37114 3.83 - 4.37: 43862 4.37 - 4.90: 72597 Nonbonded interactions: 176859 Sorted by model distance: nonbonded pdb=" OD1 ASN B 269 " pdb=" OG SER H 10 " model vdw 2.237 3.040 nonbonded pdb=" O GLY L 152 " pdb=" O2' G M 40 " model vdw 2.284 3.040 nonbonded pdb=" O ALA B 270 " pdb=" ND2 ASN H 110 " model vdw 2.285 3.120 nonbonded pdb=" O GLU H 283 " pdb=" OH TYR H 325 " model vdw 2.291 3.040 nonbonded pdb=" OE1 GLN D 229 " pdb=" O2' U M 33 " model vdw 2.291 3.040 ... (remaining 176854 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 6 through 272 or (resid 273 through 275 and (name N or nam \ e CA or name C or name O or name CB )) or resid 276 through 338)) selection = (chain 'D' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'E' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'F' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'G' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'H' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 21.210 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 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 0.071 23325 Z= 0.289 Angle : 0.993 17.136 31957 Z= 0.543 Chirality : 0.058 0.280 3331 Planarity : 0.007 0.071 3954 Dihedral : 16.386 176.078 8831 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.42 % Favored : 88.58 % Rotamer: Outliers : 0.43 % Allowed : 3.24 % Favored : 96.33 % 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: -4.46 (0.12), residues: 2855 helix: -3.30 (0.12), residues: 772 sheet: -1.45 (0.25), residues: 401 loop : -3.33 (0.12), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG E 137 TYR 0.031 0.003 TYR G 138 PHE 0.039 0.004 PHE H 336 TRP 0.065 0.005 TRP D 311 HIS 0.013 0.003 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00641 (23325) covalent geometry : angle 0.99254 (31957) hydrogen bonds : bond 0.19627 ( 768) hydrogen bonds : angle 7.97597 ( 2135) *********************** 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 272 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 264 time to evaluate : 0.739 Fit side-chains REVERT: A 242 LYS cc_start: 0.8078 (mptp) cc_final: 0.7866 (mmmt) REVERT: B 159 LEU cc_start: 0.5757 (pt) cc_final: 0.5413 (mt) REVERT: B 263 LEU cc_start: 0.7051 (mm) cc_final: 0.6710 (tp) REVERT: C 172 ARG cc_start: 0.4562 (tpt170) cc_final: 0.2757 (mtt90) REVERT: C 271 TYR cc_start: 0.3148 (p90) cc_final: 0.1680 (p90) REVERT: D 30 TRP cc_start: 0.6210 (m100) cc_final: 0.5980 (m100) REVERT: D 293 LYS cc_start: 0.7366 (tmmm) cc_final: 0.7099 (tppp) REVERT: H 175 ARG cc_start: 0.7026 (mtp85) cc_final: 0.6822 (ttm-80) REVERT: L -1 MET cc_start: 0.1241 (mmm) cc_final: -0.0394 (mmm) outliers start: 8 outliers final: 2 residues processed: 272 average time/residue: 0.7674 time to fit residues: 231.7183 Evaluate side-chains 135 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 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 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN B 104 HIS B 114 HIS B 124 GLN B 194 GLN B 305 HIS C 110 ASN C 144 ASN D 37 GLN D 83 ASN D 140 HIS D 223 GLN D 229 GLN D 324 HIS E 127 ASN E 164 HIS E 167 GLN ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 291 GLN E 324 HIS ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 ASN G 120 GLN G 129 GLN G 164 HIS H 129 GLN H 223 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.172720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.144986 restraints weight = 43417.154| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 2.22 r_work: 0.3763 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23325 Z= 0.164 Angle : 0.655 13.208 31957 Z= 0.352 Chirality : 0.044 0.217 3331 Planarity : 0.005 0.054 3954 Dihedral : 19.082 179.654 4653 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 2.49 % Allowed : 9.08 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.32 (0.14), residues: 2855 helix: -1.80 (0.16), residues: 769 sheet: -0.89 (0.26), residues: 384 loop : -2.85 (0.13), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 218 TYR 0.018 0.002 TYR F 285 PHE 0.022 0.002 PHE H 336 TRP 0.027 0.002 TRP F 311 HIS 0.009 0.002 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00361 (23325) covalent geometry : angle 0.65515 (31957) hydrogen bonds : bond 0.04515 ( 768) hydrogen bonds : angle 5.16126 ( 2135) *********************** 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 197 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 151 time to evaluate : 0.708 Fit side-chains revert: symmetry clash REVERT: A 207 ARG cc_start: 0.6880 (ttm110) cc_final: 0.6609 (tpt90) REVERT: A 234 GLU cc_start: 0.6436 (tp30) cc_final: 0.6071 (tp30) REVERT: A 242 LYS cc_start: 0.8095 (mptp) cc_final: 0.7811 (mmmt) REVERT: B 118 LEU cc_start: 0.6018 (tp) cc_final: 0.5580 (mt) REVERT: B 159 LEU cc_start: 0.5868 (pt) cc_final: 0.5215 (mt) REVERT: B 161 MET cc_start: 0.4111 (OUTLIER) cc_final: 0.3521 (ptp) REVERT: C 133 GLU cc_start: 0.4993 (OUTLIER) cc_final: 0.4427 (mm-30) REVERT: C 172 ARG cc_start: 0.3718 (tpt170) cc_final: 0.2156 (mtt90) REVERT: C 203 LEU cc_start: 0.4939 (OUTLIER) cc_final: 0.4688 (pt) REVERT: D 25 MET cc_start: 0.6467 (OUTLIER) cc_final: 0.5620 (mmt) REVERT: D 191 GLU cc_start: 0.7087 (pt0) cc_final: 0.6791 (mp0) REVERT: F 38 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7388 (pp20) REVERT: H 175 ARG cc_start: 0.7331 (mtp85) cc_final: 0.7055 (ttm-80) REVERT: H 321 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6660 (pt0) REVERT: L -1 MET cc_start: 0.1447 (mmm) cc_final: 0.0620 (mmm) outliers start: 46 outliers final: 18 residues processed: 188 average time/residue: 0.6884 time to fit residues: 146.1797 Evaluate side-chains 138 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 39 TRP Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 222 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 chunk 29 optimal weight: 60.0000 chunk 239 optimal weight: 0.8980 chunk 264 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 283 optimal weight: 40.0000 chunk 192 optimal weight: 3.9990 chunk 64 optimal weight: 0.0770 chunk 110 optimal weight: 8.9990 overall best weight: 3.9944 ------------------------------------------------------------------------------- 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 B 293 HIS B 305 HIS C 151 ASN D 140 HIS E 167 GLN ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.171273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.142830 restraints weight = 43446.642| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.76 r_work: 0.3699 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23325 Z= 0.155 Angle : 0.614 11.389 31957 Z= 0.329 Chirality : 0.043 0.212 3331 Planarity : 0.005 0.047 3954 Dihedral : 18.957 179.483 4650 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 3.08 % Allowed : 10.37 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.73 (0.15), residues: 2855 helix: -1.06 (0.18), residues: 779 sheet: -0.65 (0.26), residues: 400 loop : -2.61 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 175 TYR 0.017 0.002 TYR F 285 PHE 0.016 0.002 PHE H 336 TRP 0.020 0.002 TRP C 270 HIS 0.007 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00342 (23325) covalent geometry : angle 0.61427 (31957) hydrogen bonds : bond 0.04229 ( 768) hydrogen bonds : angle 4.76116 ( 2135) *********************** 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 188 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 131 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.3823 (mmtt) cc_final: 0.3273 (mmmt) REVERT: A 220 GLU cc_start: 0.3758 (OUTLIER) cc_final: 0.3541 (mt-10) REVERT: A 234 GLU cc_start: 0.6342 (tp30) cc_final: 0.6006 (tp30) REVERT: A 242 LYS cc_start: 0.8021 (mptp) cc_final: 0.7511 (mmmt) REVERT: B 97 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.7822 (mp) REVERT: B 118 LEU cc_start: 0.5963 (tp) cc_final: 0.5543 (mt) REVERT: B 161 MET cc_start: 0.4020 (OUTLIER) cc_final: 0.3405 (ptp) REVERT: C 121 THR cc_start: 0.1447 (OUTLIER) cc_final: 0.1012 (p) REVERT: C 203 LEU cc_start: 0.4895 (OUTLIER) cc_final: 0.4652 (pt) REVERT: D 191 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6690 (mp0) REVERT: D 267 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7638 (mm) REVERT: F 38 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7241 (pp20) REVERT: H 175 ARG cc_start: 0.7272 (mtp85) cc_final: 0.7000 (ttm-80) REVERT: H 321 GLU cc_start: 0.6934 (mm-30) cc_final: 0.6601 (pt0) REVERT: L -1 MET cc_start: 0.1256 (mmm) cc_final: 0.0437 (mmm) outliers start: 57 outliers final: 21 residues processed: 175 average time/residue: 0.7044 time to fit residues: 138.6419 Evaluate side-chains 142 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 39 TRP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 184 ARG Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 112 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 290 optimal weight: 20.0000 chunk 189 optimal weight: 9.9990 chunk 249 optimal weight: 8.9990 chunk 64 optimal weight: 30.0000 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 50.0000 chunk 74 optimal weight: 20.0000 chunk 104 optimal weight: 0.3980 chunk 171 optimal weight: 9.9990 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN B 293 HIS B 305 HIS ** C 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 HIS ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 HIS G 120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.169889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.140764 restraints weight = 43450.777| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.31 r_work: 0.3692 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23325 Z= 0.179 Angle : 0.632 12.344 31957 Z= 0.337 Chirality : 0.044 0.222 3331 Planarity : 0.005 0.047 3954 Dihedral : 18.999 179.633 4650 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 3.67 % Allowed : 11.08 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.49 (0.15), residues: 2855 helix: -0.69 (0.18), residues: 774 sheet: -0.65 (0.27), residues: 382 loop : -2.49 (0.14), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 218 TYR 0.018 0.002 TYR F 305 PHE 0.016 0.002 PHE H 336 TRP 0.018 0.002 TRP C 270 HIS 0.007 0.002 HIS B 305 Details of bonding type rmsd covalent geometry : bond 0.00403 (23325) covalent geometry : angle 0.63152 (31957) hydrogen bonds : bond 0.04346 ( 768) hydrogen bonds : angle 4.70599 ( 2135) *********************** 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 194 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 126 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.3971 (mmtt) cc_final: 0.3333 (mmmt) REVERT: A 242 LYS cc_start: 0.8065 (mptp) cc_final: 0.7678 (mmmt) REVERT: B 97 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.7862 (mp) REVERT: B 118 LEU cc_start: 0.6086 (tp) cc_final: 0.5643 (mt) REVERT: B 161 MET cc_start: 0.4230 (OUTLIER) cc_final: 0.3486 (ptp) REVERT: C 121 THR cc_start: 0.1754 (OUTLIER) cc_final: 0.1283 (p) REVERT: C 133 GLU cc_start: 0.5078 (OUTLIER) cc_final: 0.4070 (mm-30) REVERT: C 203 LEU cc_start: 0.4944 (OUTLIER) cc_final: 0.4691 (pt) REVERT: C 231 LEU cc_start: 0.1757 (OUTLIER) cc_final: -0.0613 (pt) REVERT: C 295 TYR cc_start: 0.4238 (m-10) cc_final: 0.3959 (m-80) REVERT: D 116 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8019 (m-30) REVERT: D 191 GLU cc_start: 0.6976 (pt0) cc_final: 0.6745 (mp0) REVERT: D 267 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7883 (mm) REVERT: F 38 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7471 (pp20) REVERT: H 175 ARG cc_start: 0.7416 (mtp85) cc_final: 0.7143 (ttm-80) REVERT: H 321 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6708 (pt0) REVERT: L -1 MET cc_start: 0.1257 (mmm) cc_final: 0.0428 (mmm) outliers start: 68 outliers final: 26 residues processed: 183 average time/residue: 0.6073 time to fit residues: 126.8164 Evaluate side-chains 148 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 39 TRP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 184 ARG Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 167 optimal weight: 10.0000 chunk 142 optimal weight: 0.5980 chunk 114 optimal weight: 9.9990 chunk 293 optimal weight: 20.0000 chunk 189 optimal weight: 9.9990 chunk 282 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 234 optimal weight: 10.0000 chunk 193 optimal weight: 5.9990 chunk 185 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS B 305 HIS ** C 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 HIS ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN G 241 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.170147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.141080 restraints weight = 43035.983| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.24 r_work: 0.3705 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23325 Z= 0.169 Angle : 0.616 14.224 31957 Z= 0.328 Chirality : 0.043 0.228 3331 Planarity : 0.004 0.049 3954 Dihedral : 18.973 179.440 4650 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 3.57 % Allowed : 12.43 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.15), residues: 2855 helix: -0.50 (0.19), residues: 776 sheet: -0.60 (0.26), residues: 391 loop : -2.41 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 218 TYR 0.019 0.002 TYR C 271 PHE 0.013 0.002 PHE H 336 TRP 0.018 0.002 TRP C 311 HIS 0.008 0.001 HIS B 305 Details of bonding type rmsd covalent geometry : bond 0.00378 (23325) covalent geometry : angle 0.61588 (31957) hydrogen bonds : bond 0.04142 ( 768) hydrogen bonds : angle 4.59046 ( 2135) *********************** 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 183 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 117 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.4027 (mmtp) cc_final: 0.3216 (mmmt) REVERT: A 242 LYS cc_start: 0.7981 (mptp) cc_final: 0.7587 (mmmt) REVERT: B 47 ARG cc_start: 0.6565 (tpm170) cc_final: 0.6332 (tpm170) REVERT: B 97 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7855 (mp) REVERT: B 118 LEU cc_start: 0.5977 (tp) cc_final: 0.5610 (mt) REVERT: C 121 THR cc_start: 0.1854 (OUTLIER) cc_final: 0.1395 (p) REVERT: C 133 GLU cc_start: 0.5068 (OUTLIER) cc_final: 0.4046 (mm-30) REVERT: C 203 LEU cc_start: 0.4923 (OUTLIER) cc_final: 0.4668 (pt) REVERT: C 231 LEU cc_start: 0.1767 (OUTLIER) cc_final: -0.0247 (pp) REVERT: C 271 TYR cc_start: 0.3600 (OUTLIER) cc_final: 0.3227 (p90) REVERT: C 295 TYR cc_start: 0.4487 (m-10) cc_final: 0.4118 (m-80) REVERT: D 25 MET cc_start: 0.6571 (OUTLIER) cc_final: 0.5106 (mmt) REVERT: D 116 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7900 (m-30) REVERT: D 191 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6742 (mp0) REVERT: D 267 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7908 (mm) REVERT: D 302 LEU cc_start: 0.6550 (OUTLIER) cc_final: 0.6266 (mm) REVERT: F 38 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7461 (pp20) REVERT: H 175 ARG cc_start: 0.7403 (mtp85) cc_final: 0.7118 (ttm-80) REVERT: H 321 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6708 (pt0) REVERT: L -1 MET cc_start: 0.1159 (mmm) cc_final: 0.0331 (mmm) outliers start: 66 outliers final: 28 residues processed: 172 average time/residue: 0.6045 time to fit residues: 118.9902 Evaluate side-chains 149 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 109 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 39 TRP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 184 ARG Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 86 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 90 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 152 optimal weight: 9.9990 chunk 28 optimal weight: 40.0000 chunk 48 optimal weight: 20.0000 chunk 131 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 242 optimal weight: 4.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 293 HIS B 305 HIS ** C 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN D 140 HIS ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.168082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.139030 restraints weight = 43126.499| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.30 r_work: 0.3664 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 23325 Z= 0.231 Angle : 0.689 14.979 31957 Z= 0.365 Chirality : 0.046 0.248 3331 Planarity : 0.005 0.050 3954 Dihedral : 19.060 179.608 4650 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 3.73 % Allowed : 13.07 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.38 (0.15), residues: 2855 helix: -0.52 (0.18), residues: 761 sheet: -0.59 (0.26), residues: 398 loop : -2.46 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 218 TYR 0.026 0.002 TYR C 271 PHE 0.016 0.002 PHE C 226 TRP 0.017 0.002 TRP C 311 HIS 0.008 0.002 HIS B 305 Details of bonding type rmsd covalent geometry : bond 0.00527 (23325) covalent geometry : angle 0.68868 (31957) hydrogen bonds : bond 0.04700 ( 768) hydrogen bonds : angle 4.80827 ( 2135) *********************** 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 180 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 111 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 242 LYS cc_start: 0.8030 (mptp) cc_final: 0.7597 (mmmt) REVERT: B 97 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8001 (mp) REVERT: B 118 LEU cc_start: 0.5916 (tp) cc_final: 0.5598 (mt) REVERT: C 121 THR cc_start: 0.1825 (OUTLIER) cc_final: 0.1370 (p) REVERT: C 133 GLU cc_start: 0.5178 (OUTLIER) cc_final: 0.4173 (mm-30) REVERT: C 203 LEU cc_start: 0.4969 (OUTLIER) cc_final: 0.4721 (pt) REVERT: C 231 LEU cc_start: 0.1926 (OUTLIER) cc_final: -0.0150 (pp) REVERT: D 25 MET cc_start: 0.6570 (OUTLIER) cc_final: 0.5076 (mmt) REVERT: D 191 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6850 (mp0) REVERT: D 250 ARG cc_start: 0.7236 (ppt90) cc_final: 0.6629 (mtm180) REVERT: D 267 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7947 (mm) REVERT: D 302 LEU cc_start: 0.6492 (OUTLIER) cc_final: 0.6144 (mm) REVERT: F 38 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7548 (pp20) REVERT: H 175 ARG cc_start: 0.7478 (mtp85) cc_final: 0.7166 (ttm-80) REVERT: H 321 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6789 (pt0) REVERT: L -1 MET cc_start: 0.0816 (mmm) cc_final: 0.0126 (mmm) outliers start: 69 outliers final: 33 residues processed: 173 average time/residue: 0.5856 time to fit residues: 116.5235 Evaluate side-chains 147 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 104 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 39 TRP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 174 TRP Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 184 ARG Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 62 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 258 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 181 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 106 optimal weight: 40.0000 chunk 153 optimal weight: 5.9990 chunk 187 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 293 HIS B 305 HIS ** C 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 HIS E 32 GLN ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN H 110 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.170531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.143209 restraints weight = 42903.527| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 2.10 r_work: 0.3746 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23325 Z= 0.181 Angle : 0.637 13.612 31957 Z= 0.339 Chirality : 0.044 0.244 3331 Planarity : 0.004 0.049 3954 Dihedral : 18.998 179.471 4650 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 3.30 % Allowed : 14.05 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.26 (0.15), residues: 2855 helix: -0.37 (0.19), residues: 765 sheet: -0.58 (0.26), residues: 391 loop : -2.40 (0.14), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 218 TYR 0.025 0.002 TYR C 271 PHE 0.019 0.002 PHE C 304 TRP 0.016 0.002 TRP C 311 HIS 0.007 0.001 HIS B 305 Details of bonding type rmsd covalent geometry : bond 0.00409 (23325) covalent geometry : angle 0.63710 (31957) hydrogen bonds : bond 0.04233 ( 768) hydrogen bonds : angle 4.64617 ( 2135) *********************** 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 179 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 118 time to evaluate : 0.740 Fit side-chains REVERT: A 216 LYS cc_start: 0.4173 (mmtp) cc_final: 0.3368 (mmmt) REVERT: A 237 ASN cc_start: 0.7369 (OUTLIER) cc_final: 0.6169 (t0) REVERT: A 242 LYS cc_start: 0.7917 (mptp) cc_final: 0.7469 (mmmt) REVERT: B 97 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.7949 (mp) REVERT: B 118 LEU cc_start: 0.5895 (tp) cc_final: 0.5644 (mt) REVERT: C 84 LEU cc_start: 0.1126 (OUTLIER) cc_final: 0.0912 (mp) REVERT: C 121 THR cc_start: 0.2101 (OUTLIER) cc_final: 0.1656 (p) REVERT: C 133 GLU cc_start: 0.5307 (OUTLIER) cc_final: 0.4276 (mm-30) REVERT: C 203 LEU cc_start: 0.5046 (OUTLIER) cc_final: 0.4757 (pt) REVERT: C 231 LEU cc_start: 0.1996 (OUTLIER) cc_final: -0.0151 (pp) REVERT: D 25 MET cc_start: 0.6390 (OUTLIER) cc_final: 0.4928 (mmt) REVERT: D 250 ARG cc_start: 0.6998 (ppt90) cc_final: 0.6420 (mtm180) REVERT: D 267 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7897 (mm) REVERT: D 302 LEU cc_start: 0.6521 (OUTLIER) cc_final: 0.6143 (mm) REVERT: F 38 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7492 (pp20) REVERT: F 66 LYS cc_start: 0.5601 (OUTLIER) cc_final: 0.5244 (mmtt) REVERT: F 285 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.8235 (m-80) REVERT: H 321 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6701 (pt0) REVERT: L -1 MET cc_start: 0.0606 (mmm) cc_final: -0.0128 (mmm) outliers start: 61 outliers final: 28 residues processed: 173 average time/residue: 0.5873 time to fit residues: 116.6454 Evaluate side-chains 151 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 110 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 39 TRP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 66 LYS Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 184 ARG Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 176 optimal weight: 10.0000 chunk 249 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 225 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 161 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 277 optimal weight: 50.0000 chunk 200 optimal weight: 8.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 293 HIS B 305 HIS C 324 HIS D 37 GLN ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN H 110 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.172035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.144674 restraints weight = 42903.195| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.09 r_work: 0.3766 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23325 Z= 0.147 Angle : 0.589 12.945 31957 Z= 0.314 Chirality : 0.042 0.234 3331 Planarity : 0.004 0.051 3954 Dihedral : 18.896 178.910 4650 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 3.08 % Allowed : 14.53 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.15), residues: 2855 helix: -0.18 (0.19), residues: 770 sheet: -0.54 (0.27), residues: 384 loop : -2.30 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 218 TYR 0.024 0.002 TYR C 271 PHE 0.031 0.002 PHE C 304 TRP 0.017 0.001 TRP C 311 HIS 0.007 0.001 HIS B 305 Details of bonding type rmsd covalent geometry : bond 0.00326 (23325) covalent geometry : angle 0.58935 (31957) hydrogen bonds : bond 0.03876 ( 768) hydrogen bonds : angle 4.44530 ( 2135) *********************** 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 176 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 119 time to evaluate : 0.719 Fit side-chains REVERT: A 216 LYS cc_start: 0.3981 (mmtp) cc_final: 0.3225 (mmmt) REVERT: A 237 ASN cc_start: 0.7297 (OUTLIER) cc_final: 0.6225 (t0) REVERT: A 242 LYS cc_start: 0.7871 (mptp) cc_final: 0.7534 (mmmt) REVERT: B 97 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7819 (mp) REVERT: B 118 LEU cc_start: 0.5885 (tp) cc_final: 0.5640 (mt) REVERT: C 133 GLU cc_start: 0.5263 (OUTLIER) cc_final: 0.4184 (mm-30) REVERT: C 203 LEU cc_start: 0.4961 (OUTLIER) cc_final: 0.4672 (pt) REVERT: C 231 LEU cc_start: 0.1832 (OUTLIER) cc_final: -0.0209 (pp) REVERT: D 25 MET cc_start: 0.6425 (OUTLIER) cc_final: 0.4976 (mmt) REVERT: D 267 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7858 (mm) REVERT: D 302 LEU cc_start: 0.6462 (OUTLIER) cc_final: 0.6067 (mm) REVERT: F 38 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7424 (pp20) REVERT: F 285 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.8178 (m-80) REVERT: G 238 LYS cc_start: 0.6118 (OUTLIER) cc_final: 0.5812 (tmmt) REVERT: H 321 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6657 (pt0) REVERT: L -1 MET cc_start: 0.0614 (mmm) cc_final: -0.0125 (mmm) outliers start: 57 outliers final: 28 residues processed: 170 average time/residue: 0.6173 time to fit residues: 120.0503 Evaluate side-chains 151 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 112 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 39 TRP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 266 optimal weight: 40.0000 chunk 156 optimal weight: 10.0000 chunk 292 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 12 optimal weight: 50.0000 chunk 277 optimal weight: 50.0000 chunk 50 optimal weight: 6.9990 chunk 174 optimal weight: 10.0000 chunk 210 optimal weight: 0.0770 chunk 290 optimal weight: 20.0000 chunk 75 optimal weight: 0.9990 overall best weight: 4.2148 ------------------------------------------------------------------------------- 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 293 HIS B 305 HIS ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 GLN G 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.170040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.140784 restraints weight = 43142.189| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.32 r_work: 0.3695 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23325 Z= 0.158 Angle : 0.603 13.108 31957 Z= 0.321 Chirality : 0.043 0.234 3331 Planarity : 0.004 0.051 3954 Dihedral : 18.861 179.351 4650 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 2.97 % Allowed : 15.24 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.05 (0.15), residues: 2855 helix: -0.12 (0.19), residues: 771 sheet: -0.55 (0.27), residues: 387 loop : -2.27 (0.14), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 218 TYR 0.017 0.002 TYR C 271 PHE 0.023 0.002 PHE C 304 TRP 0.017 0.002 TRP C 311 HIS 0.007 0.001 HIS B 305 Details of bonding type rmsd covalent geometry : bond 0.00354 (23325) covalent geometry : angle 0.60339 (31957) hydrogen bonds : bond 0.03974 ( 768) hydrogen bonds : angle 4.44751 ( 2135) *********************** 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 167 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 112 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.4003 (mmtp) cc_final: 0.3227 (mmmt) REVERT: A 237 ASN cc_start: 0.7279 (OUTLIER) cc_final: 0.6185 (t0) REVERT: A 242 LYS cc_start: 0.7973 (mptp) cc_final: 0.7594 (mmmt) REVERT: B 97 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7956 (mp) REVERT: B 118 LEU cc_start: 0.5882 (tp) cc_final: 0.5635 (mt) REVERT: C 121 THR cc_start: 0.1870 (OUTLIER) cc_final: 0.1401 (p) REVERT: C 133 GLU cc_start: 0.5028 (OUTLIER) cc_final: 0.3980 (mm-30) REVERT: C 203 LEU cc_start: 0.4909 (OUTLIER) cc_final: 0.4649 (pt) REVERT: C 231 LEU cc_start: 0.1845 (OUTLIER) cc_final: -0.0225 (pp) REVERT: D 25 MET cc_start: 0.6582 (OUTLIER) cc_final: 0.5118 (mmt) REVERT: D 193 ASP cc_start: 0.6447 (t0) cc_final: 0.6234 (m-30) REVERT: D 250 ARG cc_start: 0.6926 (ppt90) cc_final: 0.6430 (ptt-90) REVERT: D 267 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7903 (mm) REVERT: D 302 LEU cc_start: 0.6376 (OUTLIER) cc_final: 0.5964 (mm) REVERT: E 24 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8468 (mp) REVERT: F 38 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7487 (pp20) REVERT: F 285 TYR cc_start: 0.8696 (OUTLIER) cc_final: 0.8253 (m-80) REVERT: H 321 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6687 (pt0) REVERT: L -1 MET cc_start: 0.0704 (mmm) cc_final: -0.0029 (mmm) outliers start: 55 outliers final: 34 residues processed: 159 average time/residue: 0.6237 time to fit residues: 113.3541 Evaluate side-chains 150 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 104 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 39 TRP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 204 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 237 optimal weight: 20.0000 chunk 138 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 7 optimal weight: 0.1980 chunk 207 optimal weight: 9.9990 chunk 249 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 chunk 218 optimal weight: 30.0000 chunk 49 optimal weight: 8.9990 overall best weight: 5.8388 ------------------------------------------------------------------------------- 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 293 HIS B 305 HIS D 37 GLN D 140 HIS ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 ASN F 167 GLN G 120 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.168851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.139627 restraints weight = 42943.510| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.31 r_work: 0.3677 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23325 Z= 0.196 Angle : 0.645 13.544 31957 Z= 0.343 Chirality : 0.044 0.243 3331 Planarity : 0.005 0.051 3954 Dihedral : 18.897 179.939 4650 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 2.86 % Allowed : 15.40 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.14 (0.15), residues: 2855 helix: -0.27 (0.19), residues: 778 sheet: -0.58 (0.26), residues: 401 loop : -2.31 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 33 TYR 0.020 0.002 TYR D 285 PHE 0.024 0.002 PHE C 304 TRP 0.019 0.002 TRP C 311 HIS 0.007 0.001 HIS B 305 Details of bonding type rmsd covalent geometry : bond 0.00446 (23325) covalent geometry : angle 0.64543 (31957) hydrogen bonds : bond 0.04313 ( 768) hydrogen bonds : angle 4.58297 ( 2135) ********************** 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 158 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 105 time to evaluate : 0.841 Fit side-chains REVERT: A 216 LYS cc_start: 0.4122 (mmtp) cc_final: 0.3292 (mmmt) REVERT: A 237 ASN cc_start: 0.7303 (OUTLIER) cc_final: 0.6213 (t0) REVERT: A 242 LYS cc_start: 0.7986 (mptp) cc_final: 0.7552 (mmmt) REVERT: B 97 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8031 (mp) REVERT: B 118 LEU cc_start: 0.5856 (tp) cc_final: 0.5615 (mt) REVERT: C 121 THR cc_start: 0.1872 (OUTLIER) cc_final: 0.1412 (p) REVERT: C 133 GLU cc_start: 0.5267 (OUTLIER) cc_final: 0.4140 (mm-30) REVERT: C 203 LEU cc_start: 0.4912 (OUTLIER) cc_final: 0.4635 (pt) REVERT: C 231 LEU cc_start: 0.1962 (OUTLIER) cc_final: -0.0176 (pp) REVERT: D 25 MET cc_start: 0.6599 (OUTLIER) cc_final: 0.5121 (mmt) REVERT: D 267 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7920 (mm) REVERT: D 302 LEU cc_start: 0.6400 (OUTLIER) cc_final: 0.6068 (mm) REVERT: E 24 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8523 (mp) REVERT: F 38 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7508 (pp20) REVERT: F 285 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.8262 (m-80) REVERT: G 238 LYS cc_start: 0.6104 (OUTLIER) cc_final: 0.5782 (tmmt) REVERT: H 321 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6726 (pt0) REVERT: L -1 MET cc_start: 0.0682 (mmm) cc_final: -0.0014 (mmm) outliers start: 53 outliers final: 33 residues processed: 152 average time/residue: 0.5986 time to fit residues: 104.7781 Evaluate side-chains 148 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 102 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 39 TRP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 133 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 104 optimal weight: 0.6980 chunk 125 optimal weight: 5.9990 chunk 8 optimal weight: 40.0000 chunk 232 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 172 optimal weight: 10.0000 chunk 5 optimal weight: 50.0000 chunk 119 optimal weight: 7.9990 chunk 211 optimal weight: 5.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- 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 293 HIS B 305 HIS ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.169760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.140475 restraints weight = 42890.869| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.35 r_work: 0.3691 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23325 Z= 0.166 Angle : 0.616 13.077 31957 Z= 0.327 Chirality : 0.043 0.236 3331 Planarity : 0.004 0.050 3954 Dihedral : 18.859 179.296 4650 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 2.76 % Allowed : 15.61 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.06 (0.15), residues: 2855 helix: -0.12 (0.19), residues: 775 sheet: -0.56 (0.27), residues: 382 loop : -2.28 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 218 TYR 0.020 0.002 TYR D 285 PHE 0.023 0.002 PHE C 304 TRP 0.018 0.002 TRP C 311 HIS 0.007 0.001 HIS B 305 Details of bonding type rmsd covalent geometry : bond 0.00373 (23325) covalent geometry : angle 0.61589 (31957) hydrogen bonds : bond 0.04001 ( 768) hydrogen bonds : angle 4.48456 ( 2135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7673.93 seconds wall clock time: 131 minutes 0.49 seconds (7860.49 seconds total)