Starting phenix.real_space_refine on Wed Aug 27 01:45:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zcw_14634/08_2025/7zcw_14634_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zcw_14634/08_2025/7zcw_14634.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zcw_14634/08_2025/7zcw_14634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zcw_14634/08_2025/7zcw_14634.map" model { file = "/net/cci-nas-00/data/ceres_data/7zcw_14634/08_2025/7zcw_14634_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zcw_14634/08_2025/7zcw_14634_trim.cif" } resolution = 3.6 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= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2189 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians P 18 5.49 5 Mg 6 5.21 5 S 162 5.16 5 C 14195 2.51 5 N 3867 2.21 5 O 4322 1.98 5 H 21746 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44316 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 6658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 6658 Classifications: {'peptide': 430} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Chain: "B" Number of atoms: 6589 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 6588 Classifications: {'peptide': 426} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Conformer: "B" Number of residues, atoms: 426, 6588 Classifications: {'peptide': 426} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} bond proxies already assigned to first conformer: 6662 Chain: "C" Number of atoms: 4045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 4045 Classifications: {'peptide': 249} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 234} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 424 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 6635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 6635 Classifications: {'peptide': 428} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "F" Number of atoms: 6589 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 426, 6588 Classifications: {'peptide': 426} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Conformer: "A" Number of residues, atoms: 425, 6564 Classifications: {'peptide': 425} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 404} Chain breaks: 1 bond proxies already assigned to first conformer: 6637 Chain: "G" Number of atoms: 6589 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 6588 Classifications: {'peptide': 426} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Conformer: "B" Number of residues, atoms: 426, 6588 Classifications: {'peptide': 426} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} bond proxies already assigned to first conformer: 6662 Chain: "H" Number of atoms: 6589 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 426, 6588 Classifications: {'peptide': 426} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Conformer: "A" Number of residues, atoms: 425, 6564 Classifications: {'peptide': 425} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 404} Chain breaks: 1 bond proxies already assigned to first conformer: 6637 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N BARG F 359 " occ=0.64 ... (22 atoms not shown) pdb="HH22BARG F 359 " occ=0.64 residue: pdb=" N BARG H 359 " occ=0.68 ... (22 atoms not shown) pdb="HH22BARG H 359 " occ=0.68 Time building chain proxies: 9.67, per 1000 atoms: 0.22 Number of scatterers: 44316 At special positions: 0 Unit cell: (129.076, 121.67, 167.164, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 162 16.00 P 18 15.00 Mg 6 11.99 O 4322 8.00 N 3867 7.00 C 14195 6.00 H 21746 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5266 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 18 sheets defined 51.0% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 removed outlier: 3.641A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 51 removed outlier: 4.049A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.714A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 111 through 126 removed outlier: 4.556A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.159A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 198 removed outlier: 4.332A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU A 196 " --> pdb=" O HIS A 192 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.973A pdb=" N ILE A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 239 removed outlier: 3.859A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 287 through 297 removed outlier: 4.160A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU A 297 " --> pdb=" O ASN A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 301 removed outlier: 3.905A pdb=" N GLN A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 298 through 301' Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 383 through 400 removed outlier: 4.414A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.900A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 435 removed outlier: 4.055A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 41 through 46 removed outlier: 4.087A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 70 through 79 Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 109 through 125 removed outlier: 4.364A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 159 removed outlier: 3.725A pdb=" N THR B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 193 removed outlier: 3.670A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 193 " --> pdb=" O VAL B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.874A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 276 through 280 removed outlier: 4.584A pdb=" N GLN B 280 " --> pdb=" O GLY B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 295 through 299 removed outlier: 3.812A pdb=" N MET B 299 " --> pdb=" O ALA B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.909A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 374 through 390 removed outlier: 4.031A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG B 390 " --> pdb=" O THR B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 405 through 425 removed outlier: 3.982A pdb=" N THR B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 74 Processing helix chain 'C' and resid 77 through 86 Processing helix chain 'C' and resid 106 through 121 Processing helix chain 'C' and resid 138 through 153 removed outlier: 3.630A pdb=" N LEU C 142 " --> pdb=" O PRO C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 170 Processing helix chain 'C' and resid 200 through 203 Processing helix chain 'C' and resid 224 through 239 removed outlier: 3.733A pdb=" N TYR C 239 " --> pdb=" O SER C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 292 removed outlier: 3.563A pdb=" N ILE C 279 " --> pdb=" O LEU C 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 53 Processing helix chain 'E' and resid 10 through 29 removed outlier: 3.712A pdb=" N ALA E 19 " --> pdb=" O GLN E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 51 removed outlier: 3.549A pdb=" N ASN E 50 " --> pdb=" O ASP E 47 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR E 51 " --> pdb=" O SER E 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 47 through 51' Processing helix chain 'E' and resid 73 through 80 removed outlier: 3.624A pdb=" N GLU E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 108 removed outlier: 3.573A pdb=" N GLY E 106 " --> pdb=" O ASN E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 128 removed outlier: 3.798A pdb=" N ARG E 121 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 161 removed outlier: 4.839A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 197 removed outlier: 4.369A pdb=" N HIS E 192 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 216 removed outlier: 3.768A pdb=" N ILE E 209 " --> pdb=" O ASP E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 239 removed outlier: 3.689A pdb=" N LEU E 227 " --> pdb=" O THR E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 244 removed outlier: 3.932A pdb=" N ARG E 243 " --> pdb=" O THR E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 257 Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.771A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 removed outlier: 3.679A pdb=" N ASN E 300 " --> pdb=" O GLU E 297 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN E 301 " --> pdb=" O PRO E 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 297 through 301' Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 337 removed outlier: 3.611A pdb=" N VAL E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 400 removed outlier: 4.014A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA E 400 " --> pdb=" O ASP E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 412 removed outlier: 4.173A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY E 412 " --> pdb=" O TYR E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 435 removed outlier: 4.168A pdb=" N SER E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 29 removed outlier: 3.517A pdb=" N ASN F 14 " --> pdb=" O GLY F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 44 removed outlier: 3.774A pdb=" N GLN F 43 " --> pdb=" O SER F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 49 Processing helix chain 'F' and resid 69 through 79 removed outlier: 4.136A pdb=" N MET F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 90 Processing helix chain 'F' and resid 108 through 125 removed outlier: 3.697A pdb=" N LEU F 112 " --> pdb=" O GLU F 108 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASP F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N SER F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 159 removed outlier: 3.557A pdb=" N GLY F 148 " --> pdb=" O GLY F 144 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR F 149 " --> pdb=" O SER F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 193 removed outlier: 3.645A pdb=" N ASN F 184 " --> pdb=" O VAL F 180 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL F 193 " --> pdb=" O VAL F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 214 Processing helix chain 'F' and resid 221 through 237 removed outlier: 3.666A pdb=" N LEU F 225 " --> pdb=" O THR F 221 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR F 237 " --> pdb=" O MET F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 258 Processing helix chain 'F' and resid 285 through 294 removed outlier: 3.555A pdb=" N PHE F 294 " --> pdb=" O THR F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 308 removed outlier: 3.647A pdb=" N HIS F 307 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 337 removed outlier: 3.778A pdb=" N GLN F 334 " --> pdb=" O MET F 330 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN F 337 " --> pdb=" O VAL F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 341 Processing helix chain 'F' and resid 374 through 391 removed outlier: 4.048A pdb=" N PHE F 378 " --> pdb=" O ILE F 374 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG F 391 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 400 Processing helix chain 'F' and resid 404 through 424 removed outlier: 4.278A pdb=" N PHE F 408 " --> pdb=" O ASP F 404 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR F 409 " --> pdb=" O GLU F 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 29 Processing helix chain 'G' and resid 40 through 46 removed outlier: 4.037A pdb=" N LEU G 44 " --> pdb=" O SER G 40 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG G 46 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 49 No H-bonds generated for 'chain 'G' and resid 47 through 49' Processing helix chain 'G' and resid 70 through 79 Processing helix chain 'G' and resid 86 through 88 No H-bonds generated for 'chain 'G' and resid 86 through 88' Processing helix chain 'G' and resid 108 through 126 removed outlier: 4.148A pdb=" N LEU G 112 " --> pdb=" O GLU G 108 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASP G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N SER G 115 " --> pdb=" O GLU G 111 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL G 116 " --> pdb=" O LEU G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 159 Processing helix chain 'G' and resid 180 through 193 removed outlier: 3.587A pdb=" N ASN G 184 " --> pdb=" O VAL G 180 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN G 191 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL G 193 " --> pdb=" O VAL G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 214 removed outlier: 3.646A pdb=" N LEU G 207 " --> pdb=" O ASP G 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 237 removed outlier: 3.778A pdb=" N LEU G 225 " --> pdb=" O THR G 221 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR G 237 " --> pdb=" O MET G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 241 Processing helix chain 'G' and resid 249 through 258 Processing helix chain 'G' and resid 285 through 294 removed outlier: 3.533A pdb=" N PHE G 294 " --> pdb=" O THR G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 299 removed outlier: 4.015A pdb=" N MET G 299 " --> pdb=" O ALA G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 308 Processing helix chain 'G' and resid 322 through 337 removed outlier: 3.930A pdb=" N VAL G 326 " --> pdb=" O SER G 322 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLN G 334 " --> pdb=" O MET G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 341 Processing helix chain 'G' and resid 374 through 390 removed outlier: 3.510A pdb=" N PHE G 378 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE G 381 " --> pdb=" O LEU G 377 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG G 390 " --> pdb=" O THR G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 395 through 400 Processing helix chain 'G' and resid 405 through 424 removed outlier: 3.789A pdb=" N THR G 409 " --> pdb=" O GLU G 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 29 Processing helix chain 'H' and resid 41 through 46 removed outlier: 4.475A pdb=" N ARG H 46 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 69 through 79 removed outlier: 4.121A pdb=" N MET H 73 " --> pdb=" O GLU H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 107 through 126 removed outlier: 4.098A pdb=" N GLU H 111 " --> pdb=" O THR H 107 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU H 112 " --> pdb=" O GLU H 108 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASP H 114 " --> pdb=" O ALA H 110 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N SER H 115 " --> pdb=" O GLU H 111 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL H 116 " --> pdb=" O LEU H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 159 removed outlier: 3.823A pdb=" N THR H 149 " --> pdb=" O SER H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 193 removed outlier: 3.664A pdb=" N ASN H 184 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN H 191 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL H 193 " --> pdb=" O VAL H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 214 Processing helix chain 'H' and resid 221 through 237 removed outlier: 3.842A pdb=" N LEU H 225 " --> pdb=" O THR H 221 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR H 237 " --> pdb=" O MET H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 241 Processing helix chain 'H' and resid 249 through 258 Processing helix chain 'H' and resid 275 through 279 removed outlier: 3.961A pdb=" N SER H 278 " --> pdb=" O SER H 275 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN H 279 " --> pdb=" O ARG H 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 275 through 279' Processing helix chain 'H' and resid 285 through 294 Processing helix chain 'H' and resid 295 through 299 removed outlier: 4.131A pdb=" N MET H 299 " --> pdb=" O ALA H 296 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 308 removed outlier: 3.510A pdb=" N HIS H 307 " --> pdb=" O ASP H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 337 removed outlier: 4.137A pdb=" N GLN H 334 " --> pdb=" O MET H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 341 Processing helix chain 'H' and resid 374 through 391 removed outlier: 3.590A pdb=" N PHE H 378 " --> pdb=" O ILE H 374 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ARG H 391 " --> pdb=" O ALA H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 395 through 400 Processing helix chain 'H' and resid 404 through 425 removed outlier: 4.146A pdb=" N PHE H 408 " --> pdb=" O ASP H 404 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR H 409 " --> pdb=" O GLU H 405 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TYR H 425 " --> pdb=" O GLU H 421 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 94 removed outlier: 8.156A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 9.040A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE A 5 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N PHE A 138 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE A 7 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273 removed outlier: 4.342A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.401A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY B 132 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N SER B 138 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 163 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N HIS B 137 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N MET B 164 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B 312 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.612A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 50 through 51 removed outlier: 6.561A pdb=" N HIS C 50 " --> pdb=" O GLN C 129 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 217 through 222 removed outlier: 4.386A pdb=" N LEU C 220 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N TYR C 204 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ILE C 248 " --> pdb=" O PRO C 179 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N SER C 181 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N VAL C 246 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS C 183 " --> pdb=" O LYS C 244 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 65 through 68 removed outlier: 8.768A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLU E 3 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE E 135 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ILE E 5 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N VAL E 137 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE E 7 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER E 165 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N CYS E 200 " --> pdb=" O LYS E 166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB1, first strand: chain 'E' and resid 272 through 273 removed outlier: 4.145A pdb=" N ALA E 314 " --> pdb=" O ASN E 380 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 63 through 66 removed outlier: 8.425A pdb=" N ILE F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N HIS F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL F 66 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLN F 8 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LEU F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE F 7 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N HIS F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ALA F 9 " --> pdb=" O HIS F 137 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS F 137 " --> pdb=" O PHE F 167 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 63 through 66 removed outlier: 8.425A pdb=" N ILE F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N HIS F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL F 66 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLN F 8 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LEU F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE F 7 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N HIS F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ALA F 9 " --> pdb=" O HIS F 137 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS F 137 " --> pdb=" O PHE F 167 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER F 168 " --> pdb=" O TYR F 200 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N THR F 199 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N PHE F 265 " --> pdb=" O SER F 371 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N SER F 371 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR F 312 " --> pdb=" O ASN F 370 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.786A pdb=" N LYS F 58 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 90 through 91 removed outlier: 8.545A pdb=" N VAL G 91 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU G 65 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ILE G 64 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N HIS G 6 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N VAL G 66 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLN G 8 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLU G 3 " --> pdb=" O LEU G 130 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY G 132 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N SER G 138 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N PHE G 167 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LEU G 135 " --> pdb=" O PHE G 167 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL G 169 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N HIS G 137 " --> pdb=" O VAL G 169 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 51 through 54 Processing sheet with id=AB7, first strand: chain 'G' and resid 199 through 200 removed outlier: 6.573A pdb=" N THR G 199 " --> pdb=" O PHE G 266 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N PHE G 265 " --> pdb=" O SER G 371 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N SER G 371 " --> pdb=" O PHE G 265 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR G 312 " --> pdb=" O ASN G 370 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 91 through 92 removed outlier: 8.577A pdb=" N VAL H 91 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU H 65 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N ILE H 64 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N HIS H 6 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N VAL H 66 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N GLN H 8 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU H 3 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE H 133 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL H 5 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE H 7 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N HIS H 137 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ALA H 9 " --> pdb=" O HIS H 137 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE H 163 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS H 137 " --> pdb=" O PHE H 167 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU H 198 " --> pdb=" O MET H 164 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N ASP H 203 " --> pdb=" O PRO H 268 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N PHE H 265 " --> pdb=" O SER H 371 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N SER H 371 " --> pdb=" O PHE H 265 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR H 312 " --> pdb=" O ASN H 370 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA H 352 " --> pdb=" O ALA H 315 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 51 through 53 1024 hydrogen bonds defined for protein. 2949 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.43 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.03: 21689 1.03 - 1.24: 2366 1.24 - 1.44: 7754 1.44 - 1.65: 12742 1.65 - 1.86: 280 Bond restraints: 44831 Sorted by residual: bond pdb=" C2' G2P H 501 " pdb=" C3' G2P H 501 " ideal model delta sigma weight residual 1.528 1.243 0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C2' G2P B 501 " pdb=" C3' G2P B 501 " ideal model delta sigma weight residual 1.528 1.243 0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C2' G2P G 501 " pdb=" C3' G2P G 501 " ideal model delta sigma weight residual 1.528 1.243 0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C2' G2P F 501 " pdb=" C3' G2P F 501 " ideal model delta sigma weight residual 1.528 1.245 0.283 2.00e-02 2.50e+03 2.01e+02 bond pdb=" C3' G2P F 501 " pdb=" C4' G2P F 501 " ideal model delta sigma weight residual 1.526 1.665 -0.139 2.00e-02 2.50e+03 4.84e+01 ... (remaining 44826 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.18: 80550 5.18 - 10.36: 130 10.36 - 15.54: 11 15.54 - 20.73: 0 20.73 - 25.91: 8 Bond angle restraints: 80699 Sorted by residual: angle pdb=" C1' G2P B 501 " pdb=" N9 G2P B 501 " pdb=" C8 G2P B 501 " ideal model delta sigma weight residual 127.92 102.01 25.91 3.00e+00 1.11e-01 7.46e+01 angle pdb=" C1' G2P G 501 " pdb=" N9 G2P G 501 " pdb=" C8 G2P G 501 " ideal model delta sigma weight residual 127.92 102.13 25.79 3.00e+00 1.11e-01 7.39e+01 angle pdb=" C1' G2P B 501 " pdb=" N9 G2P B 501 " pdb=" C4 G2P B 501 " ideal model delta sigma weight residual 125.17 150.92 -25.75 3.00e+00 1.11e-01 7.37e+01 angle pdb=" C1' G2P F 501 " pdb=" N9 G2P F 501 " pdb=" C8 G2P F 501 " ideal model delta sigma weight residual 127.92 102.35 25.57 3.00e+00 1.11e-01 7.27e+01 angle pdb=" C1' G2P H 501 " pdb=" N9 G2P H 501 " pdb=" C8 G2P H 501 " ideal model delta sigma weight residual 127.92 102.36 25.56 3.00e+00 1.11e-01 7.26e+01 ... (remaining 80694 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 20494 35.38 - 70.75: 816 70.75 - 106.13: 27 106.13 - 141.51: 4 141.51 - 176.88: 4 Dihedral angle restraints: 21345 sinusoidal: 11589 harmonic: 9756 Sorted by residual: dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -113.85 -176.88 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -133.58 -157.15 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" O5' GTP E 501 " pdb=" O3A GTP E 501 " pdb=" PA GTP E 501 " pdb=" PB GTP E 501 " ideal model delta sinusoidal sigma weight residual 274.12 123.63 150.50 1 2.00e+01 2.50e-03 4.49e+01 ... (remaining 21342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2911 0.062 - 0.125: 426 0.125 - 0.187: 56 0.187 - 0.250: 5 0.250 - 0.312: 4 Chirality restraints: 3402 Sorted by residual: chirality pdb=" C3' G2P H 501 " pdb=" C2' G2P H 501 " pdb=" C4' G2P H 501 " pdb=" O3' G2P H 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.39 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" C3' G2P F 501 " pdb=" C2' G2P F 501 " pdb=" C4' G2P F 501 " pdb=" O3' G2P F 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.41 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C3' G2P G 501 " pdb=" C2' G2P G 501 " pdb=" C4' G2P G 501 " pdb=" O3' G2P G 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.41 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 3399 not shown) Planarity restraints: 6770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL H 286 " -0.068 5.00e-02 4.00e+02 9.90e-02 1.57e+01 pdb=" N PRO H 287 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO H 287 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO H 287 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 31 " -0.049 5.00e-02 4.00e+02 7.41e-02 8.78e+00 pdb=" N PRO G 32 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO G 32 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO G 32 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 320 " 0.214 9.50e-02 1.11e+02 7.17e-02 6.22e+00 pdb=" NE ARG H 320 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG H 320 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG H 320 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG H 320 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG H 320 " -0.007 2.00e-02 2.50e+03 pdb="HH12 ARG H 320 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG H 320 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG H 320 " -0.000 2.00e-02 2.50e+03 ... (remaining 6767 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 6209 2.26 - 2.85: 96539 2.85 - 3.43: 113803 3.43 - 4.02: 155514 4.02 - 4.60: 241386 Nonbonded interactions: 613451 Sorted by model distance: nonbonded pdb=" OE1 GLN F 279 " pdb="HH12 ARG F 282 " model vdw 1.678 2.450 nonbonded pdb=" O LYS H 252 " pdb="HD22 ASN H 256 " model vdw 1.704 2.450 nonbonded pdb=" OE2 GLU B 27 " pdb="HH22 ARG B 318 " model vdw 1.712 2.450 nonbonded pdb=" OD1 ASN A 186 " pdb=" HH TYR A 408 " model vdw 1.713 2.450 nonbonded pdb=" O GLY A 142 " pdb="HD22 ASN A 186 " model vdw 1.715 2.450 ... (remaining 613446 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 437 or resid 501 through 502)) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 1 through 358 or resid 361 through 502)) selection = (chain 'F' and (resid 1 through 358 or resid 361 through 502)) selection = (chain 'G' and (resid 1 through 358 or resid 361 through 502)) selection = (chain 'H' and (resid 1 through 358 or resid 361 through 502)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.200 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 37.250 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 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 : 0.008 0.285 23085 Z= 0.374 Angle : 1.014 25.907 31328 Z= 0.477 Chirality : 0.048 0.312 3402 Planarity : 0.006 0.099 4073 Dihedral : 17.262 176.884 8574 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.21 % Allowed : 12.83 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.15), residues: 2819 helix: 0.51 (0.14), residues: 1226 sheet: -1.79 (0.24), residues: 413 loop : -1.69 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 262 TYR 0.026 0.002 TYR H 310 PHE 0.019 0.002 PHE H 212 TRP 0.013 0.002 TRP C 67 HIS 0.021 0.002 HIS H 190 Details of bonding type rmsd covalent geometry : bond 0.00794 (23085) covalent geometry : angle 1.01417 (31328) hydrogen bonds : bond 0.16714 ( 1020) hydrogen bonds : angle 6.61221 ( 2949) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 68 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 464 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 459 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 265 LYS cc_start: 0.7878 (mmmt) cc_final: 0.7671 (tmmt) REVERT: C 270 ASN cc_start: 0.7379 (t0) cc_final: 0.6720 (p0) REVERT: D 50 GLU cc_start: 0.7374 (mm-30) cc_final: 0.6936 (mt-10) REVERT: F 262 ARG cc_start: 0.7941 (ttm-80) cc_final: 0.7710 (mtt90) REVERT: G 383 GLU cc_start: 0.7704 (tp30) cc_final: 0.7472 (tm-30) REVERT: G 412 GLU cc_start: 0.8129 (tp30) cc_final: 0.7852 (tm-30) REVERT: H 252 LYS cc_start: 0.5102 (mmtt) cc_final: 0.4833 (mmtt) REVERT: H 415 MET cc_start: 0.8224 (mmp) cc_final: 0.7785 (mmm) outliers start: 5 outliers final: 3 residues processed: 459 average time/residue: 0.4649 time to fit residues: 314.4712 Evaluate side-chains 443 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 440 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain F residue 178 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.0370 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 170 ASN E 8 HIS E 15 GLN E 61 HIS F 416 ASN G 307 HIS G 329 GLN G 416 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.156864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.125772 restraints weight = 83309.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.131355 restraints weight = 38979.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.133228 restraints weight = 21322.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.133366 restraints weight = 15093.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.134928 restraints weight = 14571.139| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23085 Z= 0.123 Angle : 0.555 6.321 31328 Z= 0.286 Chirality : 0.041 0.153 3402 Planarity : 0.004 0.068 4073 Dihedral : 9.935 173.586 3250 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.15 % Allowed : 12.51 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.16), residues: 2819 helix: 0.90 (0.15), residues: 1263 sheet: -1.64 (0.24), residues: 415 loop : -1.64 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 262 TYR 0.011 0.001 TYR H 159 PHE 0.014 0.001 PHE B 81 TRP 0.010 0.001 TRP E 21 HIS 0.006 0.001 HIS H 190 Details of bonding type rmsd covalent geometry : bond 0.00270 (23085) covalent geometry : angle 0.55521 (31328) hydrogen bonds : bond 0.05031 ( 1020) hydrogen bonds : angle 4.85091 ( 2949) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 68 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 467 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 439 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 ARG cc_start: 0.7866 (mtp-110) cc_final: 0.7648 (mtm110) REVERT: C 265 LYS cc_start: 0.8041 (mmmt) cc_final: 0.7373 (tmmt) REVERT: F 262 ARG cc_start: 0.7954 (ttm-80) cc_final: 0.7723 (mtt90) REVERT: G 3 GLU cc_start: 0.7492 (mp0) cc_final: 0.7063 (mp0) REVERT: G 329 GLN cc_start: 0.7042 (OUTLIER) cc_final: 0.6116 (tp40) REVERT: H 252 LYS cc_start: 0.5037 (mmtt) cc_final: 0.4822 (mmtt) REVERT: H 288 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7333 (mt-10) REVERT: H 415 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7698 (tpp) outliers start: 28 outliers final: 20 residues processed: 448 average time/residue: 0.4674 time to fit residues: 307.9511 Evaluate side-chains 441 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 419 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain G residue 92 PHE Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 329 GLN Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 415 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 277 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 90 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 chunk 217 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 220 optimal weight: 4.9990 chunk 176 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 170 ASN E 11 GLN E 301 GLN F 396 HIS F 414 ASN F 416 ASN H 11 GLN H 227 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.151395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.119272 restraints weight = 84785.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.125620 restraints weight = 41516.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.127492 restraints weight = 20800.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.127629 restraints weight = 15455.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.127943 restraints weight = 15321.902| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3605 r_free = 0.3605 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3605 r_free = 0.3605 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 23085 Z= 0.242 Angle : 0.591 6.155 31328 Z= 0.310 Chirality : 0.043 0.158 3402 Planarity : 0.005 0.063 4073 Dihedral : 10.002 179.296 3250 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.69 % Allowed : 13.04 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.15), residues: 2819 helix: 0.75 (0.14), residues: 1268 sheet: -1.75 (0.23), residues: 435 loop : -1.78 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 262 TYR 0.017 0.001 TYR H 281 PHE 0.015 0.002 PHE G 385 TRP 0.010 0.002 TRP E 21 HIS 0.006 0.001 HIS F 37 Details of bonding type rmsd covalent geometry : bond 0.00562 (23085) covalent geometry : angle 0.59147 (31328) hydrogen bonds : bond 0.05316 ( 1020) hydrogen bonds : angle 4.68166 ( 2949) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 68 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 469 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 428 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 265 LYS cc_start: 0.8117 (mmmt) cc_final: 0.7835 (tmtt) REVERT: C 270 ASN cc_start: 0.7118 (t0) cc_final: 0.6585 (p0) REVERT: G 383 GLU cc_start: 0.7781 (tp30) cc_final: 0.7412 (tm-30) REVERT: H 91 VAL cc_start: 0.8337 (OUTLIER) cc_final: 0.8051 (p) REVERT: H 252 LYS cc_start: 0.5084 (mmtt) cc_final: 0.4826 (mmtt) REVERT: H 288 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7355 (mt-10) REVERT: H 415 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7718 (tpp) outliers start: 41 outliers final: 33 residues processed: 444 average time/residue: 0.4479 time to fit residues: 290.5017 Evaluate side-chains 453 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 418 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain G residue 92 PHE Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 364 SER Chi-restraints excluded: chain H residue 415 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 96 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 153 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 278 optimal weight: 5.9990 chunk 200 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 119 optimal weight: 0.9980 chunk 185 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 GLN F 298 ASN F 348 ASN F 416 ASN H 227 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.150403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.120163 restraints weight = 83300.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.125640 restraints weight = 38009.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.127503 restraints weight = 20104.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.127841 restraints weight = 14556.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.128115 restraints weight = 14121.945| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3631 r_free = 0.3631 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3631 r_free = 0.3631 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23085 Z= 0.191 Angle : 0.553 6.024 31328 Z= 0.288 Chirality : 0.042 0.146 3402 Planarity : 0.004 0.064 4073 Dihedral : 9.956 179.588 3250 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.93 % Allowed : 13.70 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.15), residues: 2819 helix: 0.83 (0.14), residues: 1267 sheet: -1.70 (0.23), residues: 442 loop : -1.77 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 215 TYR 0.013 0.001 TYR H 281 PHE 0.013 0.001 PHE A 255 TRP 0.012 0.001 TRP E 21 HIS 0.006 0.001 HIS F 37 Details of bonding type rmsd covalent geometry : bond 0.00437 (23085) covalent geometry : angle 0.55257 (31328) hydrogen bonds : bond 0.04764 ( 1020) hydrogen bonds : angle 4.47598 ( 2949) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 68 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 471 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 424 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 TYR cc_start: 0.7987 (OUTLIER) cc_final: 0.6145 (t80) REVERT: B 349 VAL cc_start: 0.9267 (m) cc_final: 0.9059 (t) REVERT: B 417 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7687 (t0) REVERT: C 265 LYS cc_start: 0.8161 (mmmt) cc_final: 0.7853 (tmtt) REVERT: C 270 ASN cc_start: 0.7052 (t0) cc_final: 0.6521 (p0) REVERT: C 285 LYS cc_start: 0.7525 (tptm) cc_final: 0.7188 (tptt) REVERT: E 219 ILE cc_start: 0.8631 (mm) cc_final: 0.8230 (tp) REVERT: F 172 SER cc_start: 0.7744 (t) cc_final: 0.7510 (p) REVERT: F 348 ASN cc_start: 0.8386 (OUTLIER) cc_final: 0.7950 (m110) REVERT: G 329 GLN cc_start: 0.6966 (mm-40) cc_final: 0.6624 (tp40) REVERT: H 91 VAL cc_start: 0.8310 (OUTLIER) cc_final: 0.8022 (p) REVERT: H 252 LYS cc_start: 0.5113 (mmtt) cc_final: 0.4788 (mmtt) REVERT: H 288 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7474 (mt-10) REVERT: H 415 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7780 (tpp) outliers start: 47 outliers final: 36 residues processed: 448 average time/residue: 0.4339 time to fit residues: 284.1078 Evaluate side-chains 451 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 410 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 348 ASN Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain G residue 92 PHE Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 364 SER Chi-restraints excluded: chain H residue 415 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 27 optimal weight: 4.9990 chunk 278 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 233 optimal weight: 0.6980 chunk 182 optimal weight: 9.9990 chunk 239 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 232 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 416 ASN F 416 ASN G 335 ASN G 416 ASN H 227 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.151651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.121407 restraints weight = 82855.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.126647 restraints weight = 37384.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.128593 restraints weight = 19838.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.129627 restraints weight = 14453.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.129855 restraints weight = 13333.719| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23085 Z= 0.136 Angle : 0.520 5.932 31328 Z= 0.268 Chirality : 0.041 0.163 3402 Planarity : 0.004 0.064 4073 Dihedral : 9.780 177.366 3250 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.69 % Allowed : 14.32 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.16), residues: 2819 helix: 1.02 (0.15), residues: 1267 sheet: -1.67 (0.23), residues: 453 loop : -1.66 (0.17), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 276 TYR 0.010 0.001 TYR H 310 PHE 0.012 0.001 PHE A 255 TRP 0.012 0.001 TRP E 21 HIS 0.005 0.001 HIS F 37 Details of bonding type rmsd covalent geometry : bond 0.00311 (23085) covalent geometry : angle 0.51980 (31328) hydrogen bonds : bond 0.04252 ( 1020) hydrogen bonds : angle 4.26120 ( 2949) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 68 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 469 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 428 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.6164 (t80) REVERT: B 417 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7772 (t0) REVERT: C 265 LYS cc_start: 0.8157 (mmmt) cc_final: 0.7862 (tmtt) REVERT: C 270 ASN cc_start: 0.7051 (t0) cc_final: 0.6661 (p0) REVERT: C 285 LYS cc_start: 0.7600 (tptm) cc_final: 0.7285 (tptt) REVERT: E 219 ILE cc_start: 0.8648 (mm) cc_final: 0.8260 (tp) REVERT: F 158 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6738 (mp0) REVERT: H 288 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7531 (mt-10) REVERT: H 415 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7801 (tpp) outliers start: 41 outliers final: 30 residues processed: 447 average time/residue: 0.3893 time to fit residues: 254.5407 Evaluate side-chains 445 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 411 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain G residue 92 PHE Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 364 SER Chi-restraints excluded: chain H residue 415 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 158 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 254 optimal weight: 0.0270 chunk 187 optimal weight: 0.9980 chunk 188 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 chunk 253 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 overall best weight: 3.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 416 ASN E 15 GLN F 416 ASN ** G 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.150173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.119990 restraints weight = 82165.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.125328 restraints weight = 36788.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.127579 restraints weight = 19336.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.127724 restraints weight = 13667.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.127851 restraints weight = 13720.819| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23085 Z= 0.146 Angle : 0.522 5.950 31328 Z= 0.270 Chirality : 0.041 0.164 3402 Planarity : 0.004 0.065 4073 Dihedral : 9.663 176.410 3250 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.89 % Allowed : 14.40 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.16), residues: 2819 helix: 1.12 (0.15), residues: 1264 sheet: -1.58 (0.23), residues: 453 loop : -1.68 (0.17), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 276 TYR 0.010 0.001 TYR H 281 PHE 0.011 0.001 PHE A 255 TRP 0.011 0.001 TRP E 21 HIS 0.005 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00337 (23085) covalent geometry : angle 0.52228 (31328) hydrogen bonds : bond 0.04185 ( 1020) hydrogen bonds : angle 4.17470 ( 2949) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 68 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 471 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 425 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 TYR cc_start: 0.7917 (OUTLIER) cc_final: 0.6108 (t80) REVERT: B 417 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7891 (t0) REVERT: B 422 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.5884 (t80) REVERT: C 265 LYS cc_start: 0.8181 (mmmt) cc_final: 0.7839 (tmtt) REVERT: C 270 ASN cc_start: 0.7038 (t0) cc_final: 0.6531 (p0) REVERT: C 285 LYS cc_start: 0.7580 (tptm) cc_final: 0.7161 (tptt) REVERT: E 154 MET cc_start: 0.7999 (mmm) cc_final: 0.7661 (mmm) REVERT: E 219 ILE cc_start: 0.8667 (mm) cc_final: 0.8277 (tp) REVERT: F 147 MET cc_start: 0.8879 (ttp) cc_final: 0.8556 (ttt) REVERT: F 158 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6720 (mp0) REVERT: G 37 HIS cc_start: 0.8023 (m90) cc_final: 0.6457 (p90) REVERT: G 422 TYR cc_start: 0.7954 (OUTLIER) cc_final: 0.6305 (t80) REVERT: H 288 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7571 (mt-10) REVERT: H 415 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7778 (tpp) REVERT: H 421 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7964 (mt-10) outliers start: 46 outliers final: 32 residues processed: 447 average time/residue: 0.3792 time to fit residues: 247.8977 Evaluate side-chains 448 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 410 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain G residue 92 PHE Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 364 SER Chi-restraints excluded: chain H residue 415 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 147 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 159 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 193 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 chunk 263 optimal weight: 0.6980 chunk 172 optimal weight: 0.0980 chunk 134 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 416 ASN C 170 ASN E 15 GLN F 416 ASN ** G 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.153197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.123104 restraints weight = 82106.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.128406 restraints weight = 37014.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.130491 restraints weight = 19605.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.130670 restraints weight = 14059.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.130938 restraints weight = 13965.283| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23085 Z= 0.108 Angle : 0.502 6.237 31328 Z= 0.256 Chirality : 0.040 0.177 3402 Planarity : 0.004 0.070 4073 Dihedral : 9.382 171.840 3248 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.52 % Allowed : 14.93 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.16), residues: 2819 helix: 1.29 (0.15), residues: 1269 sheet: -1.56 (0.23), residues: 467 loop : -1.57 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 221 TYR 0.010 0.001 TYR C 286 PHE 0.009 0.001 PHE A 255 TRP 0.012 0.001 TRP E 21 HIS 0.004 0.001 HIS H 190 Details of bonding type rmsd covalent geometry : bond 0.00250 (23085) covalent geometry : angle 0.50152 (31328) hydrogen bonds : bond 0.03690 ( 1020) hydrogen bonds : angle 3.99561 ( 2949) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 68 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 467 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 430 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 GLU cc_start: 0.7807 (tt0) cc_final: 0.7580 (tt0) REVERT: A 432 TYR cc_start: 0.7938 (OUTLIER) cc_final: 0.6051 (t80) REVERT: B 336 LYS cc_start: 0.8213 (mmtt) cc_final: 0.7981 (mmtp) REVERT: B 417 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7896 (t0) REVERT: B 422 TYR cc_start: 0.8338 (OUTLIER) cc_final: 0.6105 (t80) REVERT: C 105 MET cc_start: 0.4665 (ppp) cc_final: 0.4439 (ppp) REVERT: C 265 LYS cc_start: 0.8145 (mmmt) cc_final: 0.7845 (tmtt) REVERT: C 270 ASN cc_start: 0.7162 (t0) cc_final: 0.6628 (p0) REVERT: C 285 LYS cc_start: 0.7615 (tptm) cc_final: 0.7114 (tptt) REVERT: C 289 ASP cc_start: 0.8253 (m-30) cc_final: 0.7762 (m-30) REVERT: F 147 MET cc_start: 0.8819 (ttp) cc_final: 0.8204 (ttt) REVERT: F 158 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6659 (mp0) REVERT: G 37 HIS cc_start: 0.8018 (m90) cc_final: 0.6444 (p90) REVERT: G 335 ASN cc_start: 0.8417 (m110) cc_final: 0.8143 (m110) REVERT: G 422 TYR cc_start: 0.8048 (OUTLIER) cc_final: 0.6451 (t80) REVERT: H 330 MET cc_start: 0.7483 (mmm) cc_final: 0.7210 (mmm) REVERT: H 415 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7783 (tpp) REVERT: H 421 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7970 (mt-10) outliers start: 37 outliers final: 27 residues processed: 449 average time/residue: 0.4007 time to fit residues: 261.9675 Evaluate side-chains 447 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 414 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 415 MET Chi-restraints excluded: chain H residue 422 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 21 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 60 optimal weight: 0.2980 chunk 25 optimal weight: 0.0870 chunk 204 optimal weight: 9.9990 chunk 139 optimal weight: 9.9990 chunk 95 optimal weight: 40.0000 chunk 115 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 overall best weight: 2.8764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 416 ASN C 170 ASN F 416 ASN ** G 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.153056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.121700 restraints weight = 83195.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.127389 restraints weight = 37718.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.129579 restraints weight = 19950.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.130224 restraints weight = 14493.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.130514 restraints weight = 13901.577| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3648 r_free = 0.3648 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3648 r_free = 0.3648 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23085 Z= 0.127 Angle : 0.506 6.049 31328 Z= 0.260 Chirality : 0.040 0.186 3402 Planarity : 0.004 0.066 4073 Dihedral : 9.299 170.285 3248 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.60 % Allowed : 14.81 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.16), residues: 2819 helix: 1.34 (0.15), residues: 1268 sheet: -1.36 (0.24), residues: 455 loop : -1.56 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 282 TYR 0.009 0.001 TYR H 281 PHE 0.019 0.001 PHE B 81 TRP 0.010 0.001 TRP E 21 HIS 0.004 0.001 HIS F 37 Details of bonding type rmsd covalent geometry : bond 0.00295 (23085) covalent geometry : angle 0.50646 (31328) hydrogen bonds : bond 0.03849 ( 1020) hydrogen bonds : angle 3.98016 ( 2949) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 68 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 460 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 421 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 TYR cc_start: 0.7937 (OUTLIER) cc_final: 0.6215 (t80) REVERT: B 417 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7898 (t0) REVERT: B 422 TYR cc_start: 0.8395 (OUTLIER) cc_final: 0.6220 (t80) REVERT: C 60 SER cc_start: 0.8333 (m) cc_final: 0.8127 (p) REVERT: C 265 LYS cc_start: 0.8197 (mmmt) cc_final: 0.7664 (tmmt) REVERT: C 270 ASN cc_start: 0.7080 (t0) cc_final: 0.6534 (p0) REVERT: C 285 LYS cc_start: 0.7543 (tptm) cc_final: 0.7200 (tptt) REVERT: E 154 MET cc_start: 0.8128 (mmm) cc_final: 0.7574 (mmm) REVERT: F 147 MET cc_start: 0.8824 (ttp) cc_final: 0.8225 (ttt) REVERT: F 158 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6658 (mp0) REVERT: F 380 ARG cc_start: 0.8109 (ptt-90) cc_final: 0.7890 (ptt180) REVERT: G 37 HIS cc_start: 0.8001 (m90) cc_final: 0.6444 (p90) REVERT: G 335 ASN cc_start: 0.8417 (m110) cc_final: 0.8147 (m110) REVERT: G 422 TYR cc_start: 0.8065 (OUTLIER) cc_final: 0.6477 (t80) REVERT: H 330 MET cc_start: 0.7523 (mmm) cc_final: 0.7263 (mmm) REVERT: H 415 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7810 (tpp) REVERT: H 421 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8017 (mt-10) outliers start: 39 outliers final: 28 residues processed: 441 average time/residue: 0.4018 time to fit residues: 261.0295 Evaluate side-chains 449 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 415 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain G residue 92 PHE Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 364 SER Chi-restraints excluded: chain H residue 415 MET Chi-restraints excluded: chain H residue 422 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 34 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 223 optimal weight: 0.0770 chunk 216 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 276 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 78 optimal weight: 0.0470 chunk 256 optimal weight: 9.9990 overall best weight: 1.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 416 ASN F 416 ASN ** G 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.154411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.123878 restraints weight = 82446.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.129741 restraints weight = 38557.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.131490 restraints weight = 19362.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.131715 restraints weight = 14625.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.132071 restraints weight = 14642.990| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23085 Z= 0.099 Angle : 0.497 6.221 31328 Z= 0.253 Chirality : 0.040 0.162 3402 Planarity : 0.004 0.066 4073 Dihedral : 9.078 165.650 3248 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.36 % Allowed : 15.06 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.16), residues: 2819 helix: 1.46 (0.15), residues: 1274 sheet: -1.31 (0.24), residues: 469 loop : -1.49 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 213 TYR 0.010 0.001 TYR G 159 PHE 0.012 0.001 PHE B 81 TRP 0.012 0.001 TRP E 21 HIS 0.004 0.001 HIS H 190 Details of bonding type rmsd covalent geometry : bond 0.00228 (23085) covalent geometry : angle 0.49688 (31328) hydrogen bonds : bond 0.03461 ( 1020) hydrogen bonds : angle 3.85164 ( 2949) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 68 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 458 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 425 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 TYR cc_start: 0.7932 (OUTLIER) cc_final: 0.6044 (t80) REVERT: B 336 LYS cc_start: 0.8200 (mmtt) cc_final: 0.7966 (mmtp) REVERT: B 422 TYR cc_start: 0.8340 (OUTLIER) cc_final: 0.6223 (t80) REVERT: C 265 LYS cc_start: 0.8111 (mmmt) cc_final: 0.7687 (tmmt) REVERT: C 285 LYS cc_start: 0.7637 (tptm) cc_final: 0.7156 (tptt) REVERT: E 219 ILE cc_start: 0.8642 (mm) cc_final: 0.8234 (tp) REVERT: F 158 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6629 (mp0) REVERT: F 380 ARG cc_start: 0.8101 (ptt-90) cc_final: 0.7871 (ptt180) REVERT: G 37 HIS cc_start: 0.7994 (m90) cc_final: 0.6437 (p90) REVERT: G 335 ASN cc_start: 0.8420 (m110) cc_final: 0.8146 (m110) REVERT: G 422 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.6484 (t80) REVERT: H 252 LYS cc_start: 0.5083 (mmtt) cc_final: 0.4267 (mmtm) REVERT: H 330 MET cc_start: 0.7438 (mmm) cc_final: 0.7134 (mmm) REVERT: H 415 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7804 (tpp) REVERT: H 421 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8032 (mt-10) outliers start: 33 outliers final: 27 residues processed: 444 average time/residue: 0.4386 time to fit residues: 284.6960 Evaluate side-chains 448 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 416 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 364 SER Chi-restraints excluded: chain H residue 415 MET Chi-restraints excluded: chain H residue 422 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 208 optimal weight: 7.9990 chunk 179 optimal weight: 0.7980 chunk 232 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 190 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 231 optimal weight: 8.9990 chunk 198 optimal weight: 10.0000 chunk 229 optimal weight: 0.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 416 ASN E 15 GLN F 416 ASN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 GLN H 227 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.152562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.121741 restraints weight = 83094.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.127549 restraints weight = 38428.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.129730 restraints weight = 19240.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.129989 restraints weight = 14307.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.130152 restraints weight = 14106.585| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23085 Z= 0.139 Angle : 0.517 6.523 31328 Z= 0.265 Chirality : 0.041 0.193 3402 Planarity : 0.004 0.066 4073 Dihedral : 9.118 165.185 3246 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.56 % Allowed : 15.30 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.16), residues: 2819 helix: 1.43 (0.15), residues: 1267 sheet: -1.34 (0.24), residues: 469 loop : -1.51 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 288 TYR 0.012 0.001 TYR G 159 PHE 0.013 0.001 PHE B 81 TRP 0.008 0.001 TRP E 21 HIS 0.004 0.001 HIS F 37 Details of bonding type rmsd covalent geometry : bond 0.00323 (23085) covalent geometry : angle 0.51727 (31328) hydrogen bonds : bond 0.03804 ( 1020) hydrogen bonds : angle 3.93484 ( 2949) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 68 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 455 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 417 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 TYR cc_start: 0.7924 (OUTLIER) cc_final: 0.6112 (t80) REVERT: B 336 LYS cc_start: 0.8236 (mmtt) cc_final: 0.7984 (mmtp) REVERT: B 422 TYR cc_start: 0.8391 (OUTLIER) cc_final: 0.6275 (t80) REVERT: C 265 LYS cc_start: 0.8160 (mmmt) cc_final: 0.7695 (tmtt) REVERT: C 270 ASN cc_start: 0.7220 (t0) cc_final: 0.6652 (p0) REVERT: E 219 ILE cc_start: 0.8674 (mm) cc_final: 0.8231 (tp) REVERT: F 158 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6620 (mp0) REVERT: F 380 ARG cc_start: 0.8107 (ptt-90) cc_final: 0.7876 (ptt180) REVERT: G 37 HIS cc_start: 0.8025 (m90) cc_final: 0.6440 (p90) REVERT: G 329 GLN cc_start: 0.6988 (OUTLIER) cc_final: 0.6407 (tp-100) REVERT: G 335 ASN cc_start: 0.8412 (m110) cc_final: 0.8121 (m110) REVERT: G 422 TYR cc_start: 0.8085 (OUTLIER) cc_final: 0.6554 (t80) REVERT: H 252 LYS cc_start: 0.4758 (mmtt) cc_final: 0.4282 (mmtt) REVERT: H 330 MET cc_start: 0.7534 (mmm) cc_final: 0.7236 (mmm) REVERT: H 415 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7832 (tpp) REVERT: H 421 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8041 (mt-10) outliers start: 38 outliers final: 30 residues processed: 441 average time/residue: 0.3929 time to fit residues: 253.7396 Evaluate side-chains 449 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 413 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain G residue 92 PHE Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 329 GLN Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 364 SER Chi-restraints excluded: chain H residue 415 MET Chi-restraints excluded: chain H residue 422 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.1589 > 50: distance: 86 - 91: 3.798 distance: 91 - 92: 4.971 distance: 92 - 93: 5.156 distance: 92 - 95: 3.186 distance: 93 - 115: 4.924 distance: 95 - 96: 5.816 distance: 95 - 104: 4.910 distance: 95 - 105: 3.436 distance: 96 - 97: 3.483 distance: 115 - 116: 4.968 distance: 116 - 117: 5.682 distance: 117 - 118: 3.208 distance: 117 - 132: 6.319 distance: 132 - 133: 8.308 distance: 133 - 134: 4.931 distance: 133 - 136: 5.669 distance: 134 - 143: 4.889 distance: 136 - 137: 3.998 distance: 143 - 144: 3.670 distance: 143 - 151: 3.307 distance: 145 - 160: 3.933 distance: 146 - 213: 3.129 distance: 160 - 161: 3.011 distance: 162 - 182: 5.288 distance: 164 - 165: 3.204 distance: 182 - 183: 4.777 distance: 183 - 184: 5.018 distance: 183 - 186: 3.843 distance: 184 - 197: 3.266 distance: 185 - 240: 6.234 distance: 186 - 187: 3.231 distance: 186 - 193: 3.453 distance: 226 - 227: 3.032 distance: 227 - 240: 8.681 distance: 240 - 241: 18.476 distance: 240 - 249: 5.745 distance: 241 - 242: 16.433 distance: 241 - 244: 18.669 distance: 241 - 250: 15.644 distance: 244 - 245: 51.159 distance: 244 - 251: 20.415 distance: 244 - 252: 18.250 distance: 245 - 246: 36.306 distance: 245 - 253: 25.158 distance: 245 - 254: 27.855 distance: 246 - 247: 47.616 distance: 246 - 248: 23.172 distance: 248 - 255: 6.974 distance: 248 - 256: 8.922