Starting phenix.real_space_refine on Sat Aug 23 23:48:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y9f_39076/08_2025/8y9f_39076.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y9f_39076/08_2025/8y9f_39076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y9f_39076/08_2025/8y9f_39076.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y9f_39076/08_2025/8y9f_39076.map" model { file = "/net/cci-nas-00/data/ceres_data/8y9f_39076/08_2025/8y9f_39076.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y9f_39076/08_2025/8y9f_39076.cif" } resolution = 3.3 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= -0.001 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 106 5.16 5 C 9755 2.51 5 N 2647 2.21 5 O 2985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s 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: 15505 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3432 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 417} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ALY:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1489 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 184} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 2, 'ASP:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 61 Chain: "D" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3356 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 406} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 3359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3359 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 410} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3350 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 406} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 391 Classifications: {'peptide': 53} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.94, per 1000 atoms: 0.19 Number of scatterers: 15505 At special positions: 0 Unit cell: (114.48, 110.24, 122.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 106 16.00 P 12 15.00 O 2985 8.00 N 2647 7.00 C 9755 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 535.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3654 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 15 sheets defined 52.7% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 39 through 51 removed outlier: 3.709A pdb=" N GLY B 43 " --> pdb=" O ALY B 40 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLY B 44 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N SER B 45 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP B 46 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP B 47 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER B 48 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE B 49 " --> pdb=" O ASP B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 110 through 129 removed outlier: 4.062A pdb=" N ILE B 114 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ASP B 116 " --> pdb=" O LYS B 112 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 162 removed outlier: 4.395A pdb=" N THR B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.754A pdb=" N ASN B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS B 192 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 Processing helix chain 'B' and resid 223 through 240 removed outlier: 3.831A pdb=" N LEU B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 277 through 282 removed outlier: 4.292A pdb=" N TYR B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 297 removed outlier: 3.634A pdb=" N PHE B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 301 removed outlier: 3.587A pdb=" N GLN B 301 " --> pdb=" O PRO B 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 298 through 301' Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 324 through 338 Processing helix chain 'B' and resid 384 through 401 removed outlier: 3.717A pdb=" N TRP B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LYS B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.830A pdb=" N TYR B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 437 removed outlier: 3.632A pdb=" N PHE B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 26 Processing helix chain 'C' and resid 31 through 50 removed outlier: 4.013A pdb=" N ALA C 35 " --> pdb=" O TYR C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 63 Processing helix chain 'C' and resid 100 through 102 No H-bonds generated for 'chain 'C' and resid 100 through 102' Processing helix chain 'C' and resid 119 through 122 removed outlier: 3.884A pdb=" N GLN C 122 " --> pdb=" O PRO C 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 119 through 122' Processing helix chain 'C' and resid 125 through 139 removed outlier: 3.706A pdb=" N LYS C 129 " --> pdb=" O GLY C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 151 through 163 removed outlier: 3.549A pdb=" N GLN C 155 " --> pdb=" O SER C 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 29 Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.892A pdb=" N LEU D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 50 removed outlier: 3.636A pdb=" N VAL D 49 " --> pdb=" O ARG D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 79 removed outlier: 3.993A pdb=" N MET D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.557A pdb=" N PHE D 85 " --> pdb=" O GLY D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 107 through 126 removed outlier: 4.063A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASN D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 159 Processing helix chain 'D' and resid 180 through 196 removed outlier: 4.071A pdb=" N HIS D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 214 Processing helix chain 'D' and resid 221 through 236 removed outlier: 3.684A pdb=" N LEU D 225 " --> pdb=" O THR D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 241 Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 285 through 294 Processing helix chain 'D' and resid 295 through 299 removed outlier: 3.562A pdb=" N MET D 299 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 308 Processing helix chain 'D' and resid 322 through 336 Processing helix chain 'D' and resid 337 through 341 Processing helix chain 'D' and resid 373 through 391 removed outlier: 3.789A pdb=" N LEU D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE D 381 " --> pdb=" O LEU D 377 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 400 removed outlier: 4.045A pdb=" N TYR D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 427 removed outlier: 3.719A pdb=" N PHE D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR D 425 " --> pdb=" O GLU D 421 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU D 427 " --> pdb=" O GLN D 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 29 removed outlier: 3.541A pdb=" N ALA E 19 " --> pdb=" O GLN E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 51 removed outlier: 3.566A pdb=" N SER E 50 " --> pdb=" O ASP E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 80 Processing helix chain 'E' and resid 81 through 86 removed outlier: 3.502A pdb=" N ARG E 84 " --> pdb=" O GLY E 81 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER E 85 " --> pdb=" O THR E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 111 through 129 removed outlier: 4.257A pdb=" N ASP E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LEU E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 161 removed outlier: 4.275A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 198 removed outlier: 3.740A pdb=" N HIS E 192 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU E 195 " --> pdb=" O THR E 191 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU E 196 " --> pdb=" O HIS E 192 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS E 197 " --> pdb=" O THR E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 216 Processing helix chain 'E' and resid 225 through 240 removed outlier: 3.903A pdb=" N ARG E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 243 No H-bonds generated for 'chain 'E' and resid 241 through 243' Processing helix chain 'E' and resid 251 through 260 Processing helix chain 'E' and resid 277 through 282 removed outlier: 3.711A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.936A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 removed outlier: 3.832A pdb=" N GLN E 301 " --> pdb=" O PRO E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 337 Processing helix chain 'E' and resid 383 through 401 removed outlier: 4.093A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS E 401 " --> pdb=" O LEU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 411 removed outlier: 4.461A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 436 removed outlier: 3.891A pdb=" N SER E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 29 Processing helix chain 'F' and resid 41 through 46 removed outlier: 4.410A pdb=" N ARG F 46 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 69 through 79 removed outlier: 4.489A pdb=" N MET F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 100 through 107 Processing helix chain 'F' and resid 107 through 126 removed outlier: 3.949A pdb=" N LEU F 112 " --> pdb=" O GLU F 108 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASP F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASN F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER F 126 " --> pdb=" O LYS F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 159 removed outlier: 3.969A pdb=" N THR F 149 " --> pdb=" O SER F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 176 Processing helix chain 'F' and resid 180 through 196 removed outlier: 3.706A pdb=" N ASN F 184 " --> pdb=" O VAL F 180 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 214 Processing helix chain 'F' and resid 221 through 237 removed outlier: 3.517A pdb=" N LEU F 225 " --> pdb=" O THR F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 258 Processing helix chain 'F' and resid 285 through 294 Processing helix chain 'F' and resid 304 through 308 Processing helix chain 'F' and resid 322 through 337 Processing helix chain 'F' and resid 338 through 341 removed outlier: 3.516A pdb=" N PHE F 341 " --> pdb=" O SER F 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 338 through 341' Processing helix chain 'F' and resid 373 through 391 removed outlier: 4.042A pdb=" N LEU F 377 " --> pdb=" O ALA F 373 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ARG F 391 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 400 removed outlier: 4.003A pdb=" N TYR F 398 " --> pdb=" O PHE F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 425 removed outlier: 4.304A pdb=" N PHE F 408 " --> pdb=" O ASP F 404 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR F 409 " --> pdb=" O GLU F 405 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET F 415 " --> pdb=" O ALA F 411 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR F 425 " --> pdb=" O GLU F 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 220 through 224 Processing helix chain 'I' and resid 225 through 232 removed outlier: 4.208A pdb=" N ASP I 229 " --> pdb=" O ASP I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 247 through 256 Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.569A pdb=" N ILE B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N MET B 67 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N GLU B 3 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N PHE B 135 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE B 5 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N VAL B 137 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE B 7 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N HIS B 139 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE B 9 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLN B 133 " --> pdb=" O ALA B 165 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N LEU B 167 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N PHE B 135 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ILE B 171 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N HIS B 139 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LYS B 166 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N PHE B 202 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLU B 168 " --> pdb=" O PHE B 202 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL B 204 " --> pdb=" O GLU B 168 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER B 170 " --> pdb=" O VAL B 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'B' and resid 269 through 272 removed outlier: 3.715A pdb=" N ALA B 374 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA B 314 " --> pdb=" O ASN B 380 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N LYS B 352 " --> pdb=" O MET B 313 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL B 315 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N GLY B 354 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEU B 317 " --> pdb=" O GLY B 354 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 2 through 3 removed outlier: 5.821A pdb=" N LEU C 84 " --> pdb=" O GLU C 75 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLU C 75 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY C 86 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE C 72 " --> pdb=" O GLN C 16 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN C 16 " --> pdb=" O ILE C 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 2 through 3 removed outlier: 7.140A pdb=" N GLY C 91 " --> pdb=" O ILE C 112 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ILE C 112 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS C 93 " --> pdb=" O MET C 110 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N MET C 110 " --> pdb=" O LYS C 93 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ALA C 146 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N MET C 110 " --> pdb=" O ALA C 146 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASP C 148 " --> pdb=" O MET C 110 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE C 112 " --> pdb=" O ASP C 148 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 98 through 99 removed outlier: 3.529A pdb=" N ASP C 99 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 91 through 92 removed outlier: 8.139A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N VAL D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N HIS D 6 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU D 3 " --> pdb=" O GLY D 132 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N GLN D 134 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N VAL D 5 " --> pdb=" O GLN D 134 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N THR D 136 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE D 7 " --> pdb=" O THR D 136 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N SER D 138 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N ALA D 9 " --> pdb=" O SER D 138 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE D 163 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N HIS D 137 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ILE D 202 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N SER D 168 " --> pdb=" O ILE D 202 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 91 through 92 removed outlier: 8.139A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N VAL D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N HIS D 6 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU D 3 " --> pdb=" O GLY D 132 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N GLN D 134 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N VAL D 5 " --> pdb=" O GLN D 134 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N THR D 136 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE D 7 " --> pdb=" O THR D 136 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N SER D 138 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N ALA D 9 " --> pdb=" O SER D 138 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE D 163 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N HIS D 137 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N MET D 164 " --> pdb=" O SER D 198 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N PHE D 200 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N THR D 166 " --> pdb=" O PHE D 200 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 268 through 270 removed outlier: 4.019A pdb=" N THR D 312 " --> pdb=" O ASN D 370 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 92 through 94 removed outlier: 7.776A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N MET E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N VAL E 66 " --> pdb=" O VAL E 4 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLU E 3 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLY E 134 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N SER E 140 " --> pdb=" O ILE E 9 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N GLN E 133 " --> pdb=" O ALA E 165 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU E 167 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N PHE E 135 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE E 169 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL E 137 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE E 171 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N HIS E 139 " --> pdb=" O ILE E 171 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 92 through 94 removed outlier: 7.776A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N MET E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N VAL E 66 " --> pdb=" O VAL E 4 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLU E 3 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLY E 134 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N SER E 140 " --> pdb=" O ILE E 9 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N GLN E 133 " --> pdb=" O ALA E 165 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU E 167 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N PHE E 135 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE E 169 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL E 137 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE E 171 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N HIS E 139 " --> pdb=" O ILE E 171 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'E' and resid 351 through 356 removed outlier: 3.562A pdb=" N ALA E 314 " --> pdb=" O ASN E 380 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 90 through 92 removed outlier: 7.836A pdb=" N VAL F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU F 65 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N VAL F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS F 6 " --> pdb=" O VAL F 64 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N VAL F 66 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N GLN F 8 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE F 7 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N HIS F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ALA F 9 " --> pdb=" O HIS F 137 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLN F 131 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ASN F 165 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N PHE F 133 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N PHE F 167 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU F 135 " --> pdb=" O PHE F 167 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL F 169 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N HIS F 137 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR F 199 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N CYS F 201 " --> pdb=" O PRO F 268 " (cutoff:3.500A) removed outlier: 11.041A pdb=" N PHE F 270 " --> pdb=" O CYS F 201 " (cutoff:3.500A) removed outlier: 13.894A pdb=" N ASP F 203 " --> pdb=" O PHE F 270 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N PHE F 265 " --> pdb=" O SER F 371 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N SER F 371 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N LYS F 350 " --> pdb=" O LEU F 311 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA F 313 " --> pdb=" O LYS F 350 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N ALA F 352 " --> pdb=" O ALA F 313 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA F 315 " --> pdb=" O ALA F 352 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N CYS F 354 " --> pdb=" O ALA F 315 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE F 317 " --> pdb=" O CYS F 354 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 51 through 53 716 hydrogen bonds defined for protein. 2046 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: 2.73 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2615 1.32 - 1.44: 4310 1.44 - 1.56: 8746 1.56 - 1.69: 16 1.69 - 1.81: 176 Bond restraints: 15863 Sorted by residual: bond pdb=" O3B G2P D 601 " pdb=" PG G2P D 601 " ideal model delta sigma weight residual 1.716 1.593 0.123 2.00e-02 2.50e+03 3.81e+01 bond pdb=" O3B G2P F 601 " pdb=" PG G2P F 601 " ideal model delta sigma weight residual 1.716 1.593 0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" O5' G2P F 601 " pdb=" PA G2P F 601 " ideal model delta sigma weight residual 1.656 1.572 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" C PRO E 222 " pdb=" O PRO E 222 " ideal model delta sigma weight residual 1.234 1.192 0.042 1.08e-02 8.57e+03 1.52e+01 bond pdb=" O5' G2P D 601 " pdb=" PA G2P D 601 " ideal model delta sigma weight residual 1.656 1.580 0.076 2.00e-02 2.50e+03 1.46e+01 ... (remaining 15858 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 21346 2.80 - 5.60: 164 5.60 - 8.40: 31 8.40 - 11.20: 11 11.20 - 14.00: 2 Bond angle restraints: 21554 Sorted by residual: angle pdb=" N ILE I 262 " pdb=" CA ILE I 262 " pdb=" C ILE I 262 " ideal model delta sigma weight residual 111.81 106.37 5.44 8.60e-01 1.35e+00 4.01e+01 angle pdb=" N ASN E 226 " pdb=" CA ASN E 226 " pdb=" C ASN E 226 " ideal model delta sigma weight residual 113.12 105.89 7.23 1.25e+00 6.40e-01 3.35e+01 angle pdb=" N TYR E 224 " pdb=" CA TYR E 224 " pdb=" C TYR E 224 " ideal model delta sigma weight residual 113.02 107.08 5.94 1.20e+00 6.94e-01 2.45e+01 angle pdb=" N ARG F 390 " pdb=" CA ARG F 390 " pdb=" C ARG F 390 " ideal model delta sigma weight residual 111.07 105.94 5.13 1.07e+00 8.73e-01 2.30e+01 angle pdb=" PA G2P D 601 " pdb=" C3A G2P D 601 " pdb=" PB G2P D 601 " ideal model delta sigma weight residual 120.83 106.83 14.00 3.00e+00 1.11e-01 2.18e+01 ... (remaining 21549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.33: 9265 35.33 - 70.66: 181 70.66 - 106.00: 8 106.00 - 141.33: 1 141.33 - 176.66: 7 Dihedral angle restraints: 9462 sinusoidal: 3773 harmonic: 5689 Sorted by residual: 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 97.46 176.66 1 2.00e+01 2.50e-03 4.80e+01 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 -115.54 -175.19 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C4' GTP B 501 " pdb=" C5' GTP B 501 " pdb=" O5' GTP B 501 " pdb=" PA GTP B 501 " ideal model delta sinusoidal sigma weight residual 260.87 105.19 155.68 1 2.00e+01 2.50e-03 4.59e+01 ... (remaining 9459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1768 0.045 - 0.090: 429 0.090 - 0.135: 153 0.135 - 0.180: 7 0.180 - 0.225: 5 Chirality restraints: 2362 Sorted by residual: chirality pdb=" C3' GTP B 501 " pdb=" C2' GTP B 501 " pdb=" C4' GTP B 501 " pdb=" O3' GTP B 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.70 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA TYR E 224 " pdb=" N TYR E 224 " pdb=" C TYR E 224 " pdb=" CB TYR E 224 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.56e-01 chirality pdb=" C3' GTP E 501 " pdb=" C2' GTP E 501 " pdb=" C4' GTP E 501 " pdb=" O3' GTP E 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.67 0.19 2.00e-01 2.50e+01 9.47e-01 ... (remaining 2359 not shown) Planarity restraints: 2803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER I 215 " 0.037 5.00e-02 4.00e+02 5.70e-02 5.20e+00 pdb=" N PRO I 216 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO I 216 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO I 216 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 89 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" C ARG C 89 " -0.039 2.00e-02 2.50e+03 pdb=" O ARG C 89 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL C 90 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP F 31 " 0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO F 32 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO F 32 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 32 " 0.031 5.00e-02 4.00e+02 ... (remaining 2800 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 3252 2.78 - 3.31: 15105 3.31 - 3.84: 26483 3.84 - 4.37: 31407 4.37 - 4.90: 54985 Nonbonded interactions: 131232 Sorted by model distance: nonbonded pdb=" OD1 ASN B 186 " pdb=" OH TYR B 408 " model vdw 2.244 3.040 nonbonded pdb=" OG SER F 95 " pdb=" OE2 GLU F 108 " model vdw 2.279 3.040 nonbonded pdb=" O SER C 80 " pdb=" OG SER C 80 " model vdw 2.287 3.040 nonbonded pdb=" NH1 ARG E 2 " pdb=" OE2 GLU F 69 " model vdw 2.303 3.120 nonbonded pdb=" OG SER B 151 " pdb=" OG1 THR B 193 " model vdw 2.311 3.040 ... (remaining 131227 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 'B' and (resid 1 through 39 or resid 47 through 59 or (resid 60 and (name \ N or name CA or name C or name O or name CB )) or resid 61 through 338 or (resi \ d 339 and (name N or name CA or name C or name O or name CB )) or resid 340 thro \ ugh 366 or (resid 367 and (name N or name CA or name C or name O or name CB )) o \ r resid 368 through 400 or (resid 401 through 403 and (name N or name CA or name \ C or name O or name CB )) or resid 404 through 501)) selection = chain 'E' } ncs_group { reference = (chain 'D' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )) or resid 158 through 358 or (resid 359 and (name N or \ name CA or name C or name O or name CB )) or resid 360 through 601)) selection = (chain 'F' and (resid 1 through 173 or (resid 174 and (name N or name CA or name \ C or name O or name CB )) or resid 175 through 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.370 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 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 : 0.004 0.123 15863 Z= 0.212 Angle : 0.667 14.002 21554 Z= 0.331 Chirality : 0.044 0.225 2362 Planarity : 0.004 0.057 2803 Dihedral : 15.170 176.661 5808 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.18 % Allowed : 0.30 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.20), residues: 1951 helix: 1.71 (0.18), residues: 853 sheet: 0.33 (0.37), residues: 238 loop : -0.76 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 64 TYR 0.031 0.001 TYR E 432 PHE 0.014 0.001 PHE F 81 TRP 0.024 0.002 TRP B 388 HIS 0.004 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00415 (15863) covalent geometry : angle 0.66678 (21554) hydrogen bonds : bond 0.15711 ( 704) hydrogen bonds : angle 5.83453 ( 2046) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 142 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: C 143 ASP cc_start: 0.8505 (m-30) cc_final: 0.8065 (t0) outliers start: 3 outliers final: 1 residues processed: 144 average time/residue: 0.1014 time to fit residues: 22.7711 Evaluate side-chains 111 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 HIS B 91 GLN C 172 ASN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 GLN D 348 ASN E 15 GLN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.043714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.035333 restraints weight = 83182.843| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 4.29 r_work: 0.2744 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15863 Z= 0.131 Angle : 0.533 7.229 21554 Z= 0.271 Chirality : 0.042 0.152 2362 Planarity : 0.004 0.053 2803 Dihedral : 11.491 174.141 2232 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.72 % Allowed : 4.82 % Favored : 94.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.19), residues: 1951 helix: 1.74 (0.18), residues: 860 sheet: -0.15 (0.35), residues: 251 loop : -0.58 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 89 TYR 0.018 0.001 TYR E 432 PHE 0.013 0.001 PHE B 255 TRP 0.013 0.001 TRP C 169 HIS 0.006 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00292 (15863) covalent geometry : angle 0.53302 (21554) hydrogen bonds : bond 0.03884 ( 704) hydrogen bonds : angle 4.54755 ( 2046) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: B 313 MET cc_start: 0.8715 (mtt) cc_final: 0.7885 (mtm) REVERT: C 134 MET cc_start: 0.9637 (tmm) cc_final: 0.9378 (tmm) REVERT: C 143 ASP cc_start: 0.9007 (m-30) cc_final: 0.8424 (t0) REVERT: D 257 MET cc_start: 0.9455 (mmm) cc_final: 0.9040 (mmm) REVERT: D 403 MET cc_start: 0.8867 (mmt) cc_final: 0.8493 (mmt) REVERT: F 233 MET cc_start: 0.9269 (mtm) cc_final: 0.8753 (mtm) REVERT: F 406 MET cc_start: 0.9221 (ppp) cc_final: 0.8529 (ppp) REVERT: I 219 ARG cc_start: 0.8634 (mmm160) cc_final: 0.7886 (mmt-90) outliers start: 12 outliers final: 6 residues processed: 122 average time/residue: 0.1079 time to fit residues: 20.5885 Evaluate side-chains 118 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain I residue 229 ASP Chi-restraints excluded: chain I residue 243 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 3 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 185 optimal weight: 3.9990 chunk 155 optimal weight: 0.0770 chunk 154 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 189 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 overall best weight: 1.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 414 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.042674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.034281 restraints weight = 85580.359| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 4.32 r_work: 0.2713 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15863 Z= 0.177 Angle : 0.530 7.070 21554 Z= 0.268 Chirality : 0.042 0.173 2362 Planarity : 0.004 0.051 2803 Dihedral : 11.153 177.597 2232 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.72 % Allowed : 7.11 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.20), residues: 1951 helix: 1.81 (0.18), residues: 863 sheet: -0.20 (0.34), residues: 261 loop : -0.55 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 53 TYR 0.013 0.001 TYR E 432 PHE 0.011 0.001 PHE B 202 TRP 0.016 0.001 TRP C 169 HIS 0.005 0.001 HIS E 8 Details of bonding type rmsd covalent geometry : bond 0.00388 (15863) covalent geometry : angle 0.53040 (21554) hydrogen bonds : bond 0.03692 ( 704) hydrogen bonds : angle 4.33401 ( 2046) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 313 MET cc_start: 0.8800 (mtt) cc_final: 0.8212 (mtm) REVERT: C 134 MET cc_start: 0.9624 (tmm) cc_final: 0.9303 (tmm) REVERT: C 143 ASP cc_start: 0.9031 (m-30) cc_final: 0.8478 (t0) REVERT: D 257 MET cc_start: 0.9403 (mmm) cc_final: 0.9042 (mmm) REVERT: E 67 MET cc_start: 0.9129 (mtp) cc_final: 0.8766 (mmt) REVERT: E 255 PHE cc_start: 0.9197 (t80) cc_final: 0.8995 (t80) REVERT: E 377 MET cc_start: 0.8890 (tmm) cc_final: 0.8662 (tmm) REVERT: F 73 MET cc_start: 0.8826 (tmm) cc_final: 0.8255 (tmm) REVERT: F 233 MET cc_start: 0.9303 (mtm) cc_final: 0.8763 (mtm) REVERT: F 403 MET cc_start: 0.8649 (mtt) cc_final: 0.8333 (mmm) REVERT: F 406 MET cc_start: 0.9250 (ppp) cc_final: 0.8523 (ppp) REVERT: I 219 ARG cc_start: 0.8725 (mmm160) cc_final: 0.8062 (mmt-90) outliers start: 12 outliers final: 8 residues processed: 118 average time/residue: 0.1071 time to fit residues: 19.5062 Evaluate side-chains 116 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain I residue 229 ASP Chi-restraints excluded: chain I residue 243 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 146 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 189 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 chunk 104 optimal weight: 7.9990 chunk 163 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 133 GLN D 278 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 233 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.042673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.034400 restraints weight = 84581.483| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 4.21 r_work: 0.2727 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15863 Z= 0.143 Angle : 0.511 7.440 21554 Z= 0.256 Chirality : 0.042 0.150 2362 Planarity : 0.003 0.050 2803 Dihedral : 10.968 175.692 2232 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.90 % Allowed : 9.40 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.20), residues: 1951 helix: 1.83 (0.18), residues: 863 sheet: -0.12 (0.34), residues: 250 loop : -0.56 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 77 TYR 0.014 0.001 TYR E 432 PHE 0.011 0.001 PHE C 157 TRP 0.018 0.001 TRP C 169 HIS 0.004 0.001 HIS E 8 Details of bonding type rmsd covalent geometry : bond 0.00317 (15863) covalent geometry : angle 0.51060 (21554) hydrogen bonds : bond 0.03435 ( 704) hydrogen bonds : angle 4.18579 ( 2046) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 313 MET cc_start: 0.8805 (mtt) cc_final: 0.8293 (mtm) REVERT: C 6 ASP cc_start: 0.9275 (m-30) cc_final: 0.8813 (t70) REVERT: C 134 MET cc_start: 0.9658 (tmm) cc_final: 0.9427 (tmm) REVERT: C 143 ASP cc_start: 0.9003 (m-30) cc_final: 0.8459 (t0) REVERT: D 257 MET cc_start: 0.9336 (mmm) cc_final: 0.9117 (mmm) REVERT: E 67 MET cc_start: 0.9140 (mtp) cc_final: 0.8861 (mmt) REVERT: E 375 VAL cc_start: 0.9301 (OUTLIER) cc_final: 0.9100 (p) REVERT: E 377 MET cc_start: 0.8881 (tmm) cc_final: 0.8264 (tmm) REVERT: F 233 MET cc_start: 0.9273 (mtm) cc_final: 0.9052 (mtp) REVERT: F 403 MET cc_start: 0.8573 (mtt) cc_final: 0.8372 (mmm) REVERT: F 406 MET cc_start: 0.9293 (ppp) cc_final: 0.8681 (ppp) REVERT: I 219 ARG cc_start: 0.8702 (mmm160) cc_final: 0.8093 (mmt-90) outliers start: 15 outliers final: 11 residues processed: 119 average time/residue: 0.1034 time to fit residues: 19.4630 Evaluate side-chains 119 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 229 ASP Chi-restraints excluded: chain I residue 243 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 94 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 GLN ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.042768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.034510 restraints weight = 84616.495| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 4.34 r_work: 0.2730 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15863 Z= 0.122 Angle : 0.499 7.986 21554 Z= 0.248 Chirality : 0.041 0.141 2362 Planarity : 0.003 0.049 2803 Dihedral : 10.833 174.004 2232 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.78 % Allowed : 10.37 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.20), residues: 1951 helix: 1.90 (0.18), residues: 863 sheet: -0.17 (0.34), residues: 255 loop : -0.53 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 77 TYR 0.012 0.001 TYR E 432 PHE 0.021 0.001 PHE E 255 TRP 0.012 0.001 TRP C 169 HIS 0.003 0.001 HIS E 8 Details of bonding type rmsd covalent geometry : bond 0.00275 (15863) covalent geometry : angle 0.49875 (21554) hydrogen bonds : bond 0.03321 ( 704) hydrogen bonds : angle 4.09670 ( 2046) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 313 MET cc_start: 0.8831 (mtt) cc_final: 0.8410 (mtm) REVERT: C 6 ASP cc_start: 0.9283 (m-30) cc_final: 0.8836 (t70) REVERT: C 134 MET cc_start: 0.9663 (tmm) cc_final: 0.9409 (tmm) REVERT: C 143 ASP cc_start: 0.9003 (m-30) cc_final: 0.8467 (t0) REVERT: D 403 MET cc_start: 0.8948 (mmt) cc_final: 0.8641 (mmt) REVERT: E 67 MET cc_start: 0.9141 (mtp) cc_final: 0.8891 (mmt) REVERT: E 255 PHE cc_start: 0.9074 (t80) cc_final: 0.8836 (t80) REVERT: E 375 VAL cc_start: 0.9323 (OUTLIER) cc_final: 0.9117 (p) REVERT: E 377 MET cc_start: 0.8944 (tmm) cc_final: 0.8329 (tmm) REVERT: F 233 MET cc_start: 0.9274 (mtm) cc_final: 0.9039 (mtp) REVERT: F 406 MET cc_start: 0.9301 (ppp) cc_final: 0.8708 (ppp) REVERT: I 219 ARG cc_start: 0.8843 (mmm160) cc_final: 0.8173 (mmt-90) outliers start: 13 outliers final: 9 residues processed: 123 average time/residue: 0.1029 time to fit residues: 20.1738 Evaluate side-chains 119 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain I residue 226 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 153 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 117 optimal weight: 0.0870 chunk 75 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 HIS E 15 GLN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.042659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.034370 restraints weight = 84648.278| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 4.25 r_work: 0.2728 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 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 0.034 15863 Z= 0.137 Angle : 0.511 9.163 21554 Z= 0.253 Chirality : 0.041 0.138 2362 Planarity : 0.003 0.049 2803 Dihedral : 10.770 173.381 2232 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.90 % Allowed : 11.15 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.20), residues: 1951 helix: 1.90 (0.18), residues: 862 sheet: -0.09 (0.34), residues: 250 loop : -0.52 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 53 TYR 0.015 0.001 TYR F 106 PHE 0.019 0.001 PHE E 255 TRP 0.012 0.001 TRP C 169 HIS 0.003 0.001 HIS E 8 Details of bonding type rmsd covalent geometry : bond 0.00303 (15863) covalent geometry : angle 0.51121 (21554) hydrogen bonds : bond 0.03292 ( 704) hydrogen bonds : angle 4.06000 ( 2046) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 6 ASP cc_start: 0.9293 (m-30) cc_final: 0.8832 (t70) REVERT: C 134 MET cc_start: 0.9669 (tmm) cc_final: 0.9404 (tmm) REVERT: C 143 ASP cc_start: 0.9037 (m-30) cc_final: 0.8517 (t0) REVERT: D 257 MET cc_start: 0.9519 (mmm) cc_final: 0.9311 (mmm) REVERT: D 403 MET cc_start: 0.8926 (mmt) cc_final: 0.8638 (mmt) REVERT: E 255 PHE cc_start: 0.9123 (t80) cc_final: 0.8892 (t80) REVERT: E 375 VAL cc_start: 0.9305 (OUTLIER) cc_final: 0.9083 (p) REVERT: E 377 MET cc_start: 0.8930 (tmm) cc_final: 0.8335 (tmm) REVERT: F 233 MET cc_start: 0.9261 (mtm) cc_final: 0.9012 (mtp) REVERT: F 406 MET cc_start: 0.9294 (ppp) cc_final: 0.8720 (ppp) REVERT: I 219 ARG cc_start: 0.8886 (mmm160) cc_final: 0.8200 (mmt-90) outliers start: 15 outliers final: 11 residues processed: 121 average time/residue: 0.0990 time to fit residues: 19.1404 Evaluate side-chains 122 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain I residue 243 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 24 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 189 optimal weight: 20.0000 chunk 192 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 26 optimal weight: 0.0050 chunk 163 optimal weight: 4.9990 chunk 151 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 overall best weight: 1.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.041977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.033821 restraints weight = 84905.398| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 4.26 r_work: 0.2710 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15863 Z= 0.173 Angle : 0.537 8.731 21554 Z= 0.266 Chirality : 0.042 0.146 2362 Planarity : 0.003 0.049 2803 Dihedral : 10.780 174.835 2232 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.96 % Allowed : 12.00 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.20), residues: 1951 helix: 1.89 (0.18), residues: 862 sheet: -0.17 (0.34), residues: 250 loop : -0.51 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 53 TYR 0.013 0.001 TYR E 432 PHE 0.019 0.001 PHE E 255 TRP 0.011 0.001 TRP E 21 HIS 0.006 0.001 HIS D 137 Details of bonding type rmsd covalent geometry : bond 0.00378 (15863) covalent geometry : angle 0.53693 (21554) hydrogen bonds : bond 0.03471 ( 704) hydrogen bonds : angle 4.11210 ( 2046) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 6 ASP cc_start: 0.9301 (m-30) cc_final: 0.8841 (t70) REVERT: C 134 MET cc_start: 0.9678 (tmm) cc_final: 0.9428 (tmm) REVERT: C 143 ASP cc_start: 0.9071 (m-30) cc_final: 0.8581 (t0) REVERT: C 159 GLU cc_start: 0.9318 (mm-30) cc_final: 0.9048 (mm-30) REVERT: D 233 MET cc_start: 0.9324 (mtt) cc_final: 0.9081 (mtp) REVERT: D 403 MET cc_start: 0.8915 (mmt) cc_final: 0.8619 (mmt) REVERT: E 67 MET cc_start: 0.9171 (mtp) cc_final: 0.8894 (mmt) REVERT: E 255 PHE cc_start: 0.9158 (t80) cc_final: 0.8931 (t80) REVERT: E 375 VAL cc_start: 0.9332 (OUTLIER) cc_final: 0.9105 (p) REVERT: E 377 MET cc_start: 0.8969 (tmm) cc_final: 0.8424 (tmm) REVERT: F 152 ILE cc_start: 0.9617 (OUTLIER) cc_final: 0.9313 (pt) REVERT: F 233 MET cc_start: 0.9283 (mtm) cc_final: 0.9035 (mtp) REVERT: F 406 MET cc_start: 0.9300 (ppp) cc_final: 0.8719 (ppp) REVERT: I 219 ARG cc_start: 0.8901 (mmm160) cc_final: 0.8697 (mmt90) outliers start: 16 outliers final: 13 residues processed: 117 average time/residue: 0.1090 time to fit residues: 20.3665 Evaluate side-chains 125 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain I residue 229 ASP Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 249 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 112 optimal weight: 0.0040 chunk 126 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 190 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 HIS ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.042860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.034722 restraints weight = 83535.993| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 4.30 r_work: 0.2743 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15863 Z= 0.105 Angle : 0.519 11.581 21554 Z= 0.253 Chirality : 0.041 0.163 2362 Planarity : 0.003 0.049 2803 Dihedral : 10.685 171.453 2232 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.02 % Allowed : 12.36 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.20), residues: 1951 helix: 1.95 (0.18), residues: 862 sheet: -0.16 (0.34), residues: 250 loop : -0.47 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 53 TYR 0.013 0.001 TYR E 432 PHE 0.018 0.001 PHE E 255 TRP 0.010 0.001 TRP C 169 HIS 0.003 0.001 HIS D 137 Details of bonding type rmsd covalent geometry : bond 0.00239 (15863) covalent geometry : angle 0.51923 (21554) hydrogen bonds : bond 0.03182 ( 704) hydrogen bonds : angle 4.02772 ( 2046) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 6 ASP cc_start: 0.9300 (OUTLIER) cc_final: 0.8836 (t70) REVERT: C 57 MET cc_start: 0.9284 (mtp) cc_final: 0.8935 (mtm) REVERT: C 134 MET cc_start: 0.9676 (tmm) cc_final: 0.9417 (tmm) REVERT: C 143 ASP cc_start: 0.9056 (m-30) cc_final: 0.8563 (t0) REVERT: C 159 GLU cc_start: 0.9305 (mm-30) cc_final: 0.9050 (mm-30) REVERT: D 233 MET cc_start: 0.9332 (mtt) cc_final: 0.9100 (mtp) REVERT: D 403 MET cc_start: 0.8832 (mmt) cc_final: 0.8571 (mmt) REVERT: E 67 MET cc_start: 0.9140 (mtp) cc_final: 0.8907 (mmt) REVERT: E 239 THR cc_start: 0.9512 (OUTLIER) cc_final: 0.9267 (p) REVERT: E 255 PHE cc_start: 0.9131 (t80) cc_final: 0.8718 (t80) REVERT: E 375 VAL cc_start: 0.9331 (OUTLIER) cc_final: 0.9108 (p) REVERT: E 377 MET cc_start: 0.8972 (tmm) cc_final: 0.8478 (tmm) REVERT: F 31 ASP cc_start: 0.9546 (OUTLIER) cc_final: 0.9206 (t0) REVERT: F 233 MET cc_start: 0.9245 (mtm) cc_final: 0.8973 (mtp) REVERT: F 403 MET cc_start: 0.8781 (mmm) cc_final: 0.8118 (mmm) REVERT: F 406 MET cc_start: 0.9324 (ppp) cc_final: 0.8716 (ppp) REVERT: I 219 ARG cc_start: 0.8882 (mmm160) cc_final: 0.8680 (mmt90) outliers start: 17 outliers final: 9 residues processed: 127 average time/residue: 0.1185 time to fit residues: 23.8044 Evaluate side-chains 126 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 249 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 29 optimal weight: 0.8980 chunk 157 optimal weight: 7.9990 chunk 172 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 112 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.041469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.033375 restraints weight = 86826.916| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 4.20 r_work: 0.2694 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15863 Z= 0.230 Angle : 0.592 10.602 21554 Z= 0.292 Chirality : 0.042 0.155 2362 Planarity : 0.004 0.049 2803 Dihedral : 10.814 177.485 2232 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.15 % Allowed : 12.42 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.20), residues: 1951 helix: 1.82 (0.18), residues: 865 sheet: -0.22 (0.34), residues: 252 loop : -0.49 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 260 TYR 0.014 0.001 TYR E 432 PHE 0.019 0.001 PHE B 255 TRP 0.012 0.001 TRP E 21 HIS 0.009 0.001 HIS D 137 Details of bonding type rmsd covalent geometry : bond 0.00497 (15863) covalent geometry : angle 0.59157 (21554) hydrogen bonds : bond 0.03659 ( 704) hydrogen bonds : angle 4.18800 ( 2046) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 ASP cc_start: 0.9255 (m-30) cc_final: 0.8826 (t70) REVERT: C 57 MET cc_start: 0.9295 (mtp) cc_final: 0.8895 (mtm) REVERT: C 134 MET cc_start: 0.9690 (tmm) cc_final: 0.9392 (tmm) REVERT: C 159 GLU cc_start: 0.9285 (mm-30) cc_final: 0.9004 (mm-30) REVERT: D 257 MET cc_start: 0.9554 (mmm) cc_final: 0.9237 (mmm) REVERT: D 403 MET cc_start: 0.9003 (mmt) cc_final: 0.8716 (mmt) REVERT: E 67 MET cc_start: 0.9188 (mtp) cc_final: 0.8795 (mmt) REVERT: E 239 THR cc_start: 0.9553 (OUTLIER) cc_final: 0.9335 (p) REVERT: E 255 PHE cc_start: 0.9162 (t80) cc_final: 0.8835 (t80) REVERT: E 375 VAL cc_start: 0.9328 (OUTLIER) cc_final: 0.9089 (p) REVERT: E 377 MET cc_start: 0.9001 (tmm) cc_final: 0.8447 (tmm) REVERT: F 31 ASP cc_start: 0.9540 (OUTLIER) cc_final: 0.9172 (t70) REVERT: F 233 MET cc_start: 0.9298 (mtm) cc_final: 0.9053 (mtp) REVERT: F 403 MET cc_start: 0.8898 (mmm) cc_final: 0.8224 (mmm) REVERT: F 406 MET cc_start: 0.9335 (ppp) cc_final: 0.8731 (ppp) REVERT: I 219 ARG cc_start: 0.8895 (mmm160) cc_final: 0.8100 (mmt90) outliers start: 19 outliers final: 11 residues processed: 121 average time/residue: 0.1223 time to fit residues: 23.4947 Evaluate side-chains 122 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 34 optimal weight: 0.8980 chunk 7 optimal weight: 20.0000 chunk 83 optimal weight: 0.0060 chunk 150 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 125 optimal weight: 0.2980 chunk 6 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.042979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.034741 restraints weight = 84684.018| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 4.30 r_work: 0.2748 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15863 Z= 0.100 Angle : 0.535 10.843 21554 Z= 0.260 Chirality : 0.041 0.145 2362 Planarity : 0.003 0.048 2803 Dihedral : 10.682 172.294 2232 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.72 % Allowed : 12.90 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.20), residues: 1951 helix: 1.92 (0.18), residues: 865 sheet: -0.21 (0.34), residues: 251 loop : -0.41 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 77 TYR 0.015 0.001 TYR E 432 PHE 0.020 0.001 PHE B 255 TRP 0.011 0.001 TRP C 169 HIS 0.003 0.001 HIS D 137 Details of bonding type rmsd covalent geometry : bond 0.00227 (15863) covalent geometry : angle 0.53471 (21554) hydrogen bonds : bond 0.03159 ( 704) hydrogen bonds : angle 4.03751 ( 2046) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 6 ASP cc_start: 0.9311 (m-30) cc_final: 0.8798 (t70) REVERT: C 57 MET cc_start: 0.9275 (mtp) cc_final: 0.8878 (mtm) REVERT: C 134 MET cc_start: 0.9678 (tmm) cc_final: 0.9377 (tmm) REVERT: C 143 ASP cc_start: 0.8837 (m-30) cc_final: 0.8293 (t0) REVERT: C 159 GLU cc_start: 0.9295 (mm-30) cc_final: 0.9037 (mm-30) REVERT: D 233 MET cc_start: 0.9312 (mtt) cc_final: 0.9080 (mtp) REVERT: D 257 MET cc_start: 0.9528 (mmm) cc_final: 0.9268 (mmm) REVERT: D 403 MET cc_start: 0.8830 (mmt) cc_final: 0.8433 (mmt) REVERT: E 239 THR cc_start: 0.9499 (OUTLIER) cc_final: 0.9253 (p) REVERT: E 255 PHE cc_start: 0.9089 (t80) cc_final: 0.8704 (t80) REVERT: E 377 MET cc_start: 0.8995 (tmm) cc_final: 0.8542 (tmm) REVERT: F 31 ASP cc_start: 0.9541 (OUTLIER) cc_final: 0.9171 (t70) REVERT: F 233 MET cc_start: 0.9262 (mtm) cc_final: 0.8970 (mtp) REVERT: F 403 MET cc_start: 0.8843 (mmm) cc_final: 0.8232 (mmm) REVERT: F 406 MET cc_start: 0.9329 (ppp) cc_final: 0.8763 (ppp) REVERT: I 217 ILE cc_start: 0.8562 (mp) cc_final: 0.7995 (mp) REVERT: I 219 ARG cc_start: 0.8829 (mmm160) cc_final: 0.8309 (mmt-90) outliers start: 12 outliers final: 8 residues processed: 121 average time/residue: 0.1201 time to fit residues: 22.9346 Evaluate side-chains 122 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 179 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 176 optimal weight: 0.0670 chunk 83 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.042859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.034622 restraints weight = 84699.455| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 4.30 r_work: 0.2744 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15863 Z= 0.113 Angle : 0.540 12.575 21554 Z= 0.262 Chirality : 0.041 0.140 2362 Planarity : 0.003 0.049 2803 Dihedral : 10.611 170.506 2232 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.72 % Allowed : 13.02 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.20), residues: 1951 helix: 1.92 (0.18), residues: 865 sheet: -0.19 (0.34), residues: 251 loop : -0.40 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 77 TYR 0.014 0.001 TYR E 432 PHE 0.017 0.001 PHE E 255 TRP 0.044 0.001 TRP B 388 HIS 0.012 0.001 HIS E 8 Details of bonding type rmsd covalent geometry : bond 0.00258 (15863) covalent geometry : angle 0.54016 (21554) hydrogen bonds : bond 0.03219 ( 704) hydrogen bonds : angle 4.00923 ( 2046) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3160.81 seconds wall clock time: 55 minutes 15.69 seconds (3315.69 seconds total)