Starting phenix.real_space_refine on Mon Nov 18 04:58:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y9f_39076/11_2024/8y9f_39076.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y9f_39076/11_2024/8y9f_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y9f_39076/11_2024/8y9f_39076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y9f_39076/11_2024/8y9f_39076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y9f_39076/11_2024/8y9f_39076.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y9f_39076/11_2024/8y9f_39076.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: {'GLN:plan1': 2, 'GLU:plan': 7, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4} 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: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 2} 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: 10.83, per 1000 atoms: 0.70 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: 4.09 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.87 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: 5.41 Time building geometry restraints manager: 4.68 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 439 or resid 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 427 or resid 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 427 or resid 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: 2.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 37.660 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.720 ------------------------------------------------------------------------------- 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= 0.277 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 : 9.51 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.024 0.002 TRP B 388 HIS 0.004 0.001 HIS E 88 PHE 0.014 0.001 PHE F 81 TYR 0.031 0.001 TYR E 432 ARG 0.004 0.000 ARG E 64 *********************** 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 : 2.036 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: 0.2596 time to fit residues: 57.9824 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 : 1.813 ------------------------------------------------------------------------------- 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 163 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 113 optimal weight: 0.0980 chunk 176 optimal weight: 7.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 ASN D 329 GLN D 348 ASN E 15 GLN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15863 Z= 0.218 Angle : 0.539 7.194 21554 Z= 0.274 Chirality : 0.043 0.163 2362 Planarity : 0.004 0.052 2803 Dihedral : 11.455 174.850 2232 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.72 % Allowed : 4.76 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.20), residues: 1951 helix: 1.74 (0.18), residues: 860 sheet: -0.13 (0.35), residues: 259 loop : -0.60 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.005 0.001 HIS E 8 PHE 0.013 0.001 PHE B 255 TYR 0.018 0.001 TYR E 432 ARG 0.003 0.000 ARG C 53 *********************** 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 : 1.738 Fit side-chains revert: symmetry clash REVERT: C 133 GLU cc_start: 0.8914 (tp30) cc_final: 0.8703 (tp30) REVERT: C 134 MET cc_start: 0.8920 (tmm) cc_final: 0.8608 (tmm) REVERT: C 143 ASP cc_start: 0.8477 (m-30) cc_final: 0.8051 (t0) outliers start: 12 outliers final: 6 residues processed: 123 average time/residue: 0.2585 time to fit residues: 50.5772 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 : 1.799 ------------------------------------------------------------------------------- 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 97 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 chunk 190 optimal weight: 4.9990 chunk 157 optimal weight: 10.0000 chunk 175 optimal weight: 0.4980 chunk 60 optimal weight: 0.9990 chunk 141 optimal weight: 0.0980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN D 414 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 ASN ** I 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15863 Z= 0.158 Angle : 0.496 6.955 21554 Z= 0.250 Chirality : 0.042 0.143 2362 Planarity : 0.003 0.048 2803 Dihedral : 11.027 174.189 2232 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.72 % Allowed : 7.29 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.20), residues: 1951 helix: 1.85 (0.18), residues: 861 sheet: -0.06 (0.35), residues: 250 loop : -0.57 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 169 HIS 0.004 0.001 HIS E 8 PHE 0.009 0.001 PHE B 255 TYR 0.014 0.001 TYR E 432 ARG 0.003 0.000 ARG C 53 *********************** 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 133 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 133 GLU cc_start: 0.8864 (tp30) cc_final: 0.8654 (tp30) REVERT: C 134 MET cc_start: 0.8878 (tmm) cc_final: 0.8493 (tmm) REVERT: C 143 ASP cc_start: 0.8409 (m-30) cc_final: 0.8033 (t0) REVERT: D 257 MET cc_start: 0.8524 (mmm) cc_final: 0.8275 (mmm) REVERT: F 73 MET cc_start: 0.7743 (tmm) cc_final: 0.6726 (tmm) REVERT: F 233 MET cc_start: 0.7771 (mtm) cc_final: 0.7508 (mtm) REVERT: F 406 MET cc_start: 0.7589 (ppp) cc_final: 0.6801 (ppp) outliers start: 12 outliers final: 7 residues processed: 121 average time/residue: 0.2800 time to fit residues: 52.5946 Evaluate side-chains 116 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 1.864 ------------------------------------------------------------------------------- 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 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 220 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 174 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 187 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 15 GLN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15863 Z= 0.295 Angle : 0.542 7.046 21554 Z= 0.273 Chirality : 0.042 0.150 2362 Planarity : 0.004 0.049 2803 Dihedral : 10.990 177.634 2232 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.02 % Allowed : 8.68 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.20), residues: 1951 helix: 1.83 (0.18), residues: 861 sheet: -0.04 (0.34), residues: 247 loop : -0.55 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 169 HIS 0.011 0.001 HIS E 8 PHE 0.012 0.001 PHE C 157 TYR 0.013 0.001 TYR F 106 ARG 0.013 0.000 ARG F 77 *********************** 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 127 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 133 GLU cc_start: 0.8918 (tp30) cc_final: 0.8717 (tp30) REVERT: C 134 MET cc_start: 0.8937 (tmm) cc_final: 0.8614 (tmm) REVERT: C 143 ASP cc_start: 0.8424 (m-30) cc_final: 0.8031 (t0) REVERT: F 233 MET cc_start: 0.7848 (mtm) cc_final: 0.7615 (mtp) REVERT: F 406 MET cc_start: 0.7742 (ppp) cc_final: 0.7206 (ppp) outliers start: 17 outliers final: 13 residues processed: 115 average time/residue: 0.2518 time to fit residues: 46.6503 Evaluate side-chains 120 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 1.870 ------------------------------------------------------------------------------- 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 53 ARG Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 130 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 156 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 129 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 HIS ** I 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15863 Z= 0.270 Angle : 0.535 7.715 21554 Z= 0.268 Chirality : 0.042 0.146 2362 Planarity : 0.003 0.049 2803 Dihedral : 10.935 178.005 2232 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.84 % Allowed : 10.55 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.20), residues: 1951 helix: 1.83 (0.18), residues: 862 sheet: -0.32 (0.33), residues: 269 loop : -0.49 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 169 HIS 0.009 0.001 HIS E 8 PHE 0.010 0.001 PHE C 157 TYR 0.013 0.001 TYR F 106 ARG 0.008 0.000 ARG I 260 *********************** 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 123 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 134 MET cc_start: 0.8941 (tmm) cc_final: 0.8645 (tmm) REVERT: C 143 ASP cc_start: 0.8441 (m-30) cc_final: 0.8056 (t0) REVERT: F 233 MET cc_start: 0.7841 (mtm) cc_final: 0.7601 (mtp) REVERT: F 403 MET cc_start: 0.7658 (mmm) cc_final: 0.7049 (mmm) REVERT: F 406 MET cc_start: 0.7656 (ppp) cc_final: 0.7110 (ppp) outliers start: 14 outliers final: 13 residues processed: 113 average time/residue: 0.2599 time to fit residues: 46.4916 Evaluate side-chains 119 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 1.935 ------------------------------------------------------------------------------- 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 53 ARG 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 255 PHE Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain I residue 229 ASP Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 251 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 63 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 HIS ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1744 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= 0.185 Angle : 0.520 11.295 21554 Z= 0.256 Chirality : 0.041 0.143 2362 Planarity : 0.003 0.049 2803 Dihedral : 10.840 175.475 2232 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.84 % Allowed : 11.57 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.20), residues: 1951 helix: 1.89 (0.18), residues: 863 sheet: -0.21 (0.34), residues: 250 loop : -0.54 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 169 HIS 0.004 0.001 HIS E 8 PHE 0.010 0.001 PHE C 157 TYR 0.013 0.001 TYR E 432 ARG 0.005 0.000 ARG F 77 *********************** 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 125 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 6 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8147 (t70) REVERT: C 134 MET cc_start: 0.8919 (tmm) cc_final: 0.8699 (tmm) REVERT: C 143 ASP cc_start: 0.8440 (m-30) cc_final: 0.8029 (t0) REVERT: D 257 MET cc_start: 0.8594 (mmm) cc_final: 0.8393 (mmm) REVERT: F 233 MET cc_start: 0.7791 (mtm) cc_final: 0.7538 (mtp) REVERT: F 406 MET cc_start: 0.7612 (ppp) cc_final: 0.7171 (ppp) outliers start: 14 outliers final: 9 residues processed: 116 average time/residue: 0.2550 time to fit residues: 47.3364 Evaluate side-chains 117 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 1.859 ------------------------------------------------------------------------------- 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 6 ASP Chi-restraints excluded: chain C residue 53 ARG 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 145 THR Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 135 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 180 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 104 optimal weight: 8.9990 chunk 186 optimal weight: 0.4980 chunk 117 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 86 optimal weight: 0.0170 chunk 115 optimal weight: 0.9980 overall best weight: 0.6818 ------------------------------------------------------------------------------- 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 ** 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** ** I 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1864 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= 0.155 Angle : 0.519 11.065 21554 Z= 0.253 Chirality : 0.041 0.154 2362 Planarity : 0.003 0.049 2803 Dihedral : 10.698 171.862 2232 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.72 % Allowed : 12.30 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.20), residues: 1951 helix: 1.92 (0.18), residues: 864 sheet: -0.19 (0.34), residues: 247 loop : -0.51 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 169 HIS 0.003 0.001 HIS F 227 PHE 0.010 0.001 PHE C 157 TYR 0.013 0.001 TYR E 432 ARG 0.005 0.000 ARG F 77 *********************** 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 130 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 6 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8113 (t70) REVERT: C 134 MET cc_start: 0.8935 (tmm) cc_final: 0.8733 (tmm) REVERT: C 143 ASP cc_start: 0.8443 (m-30) cc_final: 0.8036 (t0) REVERT: F 233 MET cc_start: 0.7743 (mtm) cc_final: 0.7499 (mtp) REVERT: F 406 MET cc_start: 0.7628 (ppp) cc_final: 0.7191 (ppp) outliers start: 12 outliers final: 6 residues processed: 122 average time/residue: 0.2629 time to fit residues: 50.3882 Evaluate side-chains 120 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain C residue 6 ASP 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 F residue 113 VAL Chi-restraints excluded: chain I residue 243 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 74 optimal weight: 0.3980 chunk 111 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 36 optimal weight: 0.0570 chunk 118 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 chunk 17 optimal weight: 0.0370 chunk 146 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 179 optimal weight: 0.7980 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 GLN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 GLN ** 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** I 233 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15863 Z= 0.142 Angle : 0.533 10.734 21554 Z= 0.255 Chirality : 0.041 0.146 2362 Planarity : 0.003 0.049 2803 Dihedral : 10.535 166.740 2232 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.60 % Allowed : 12.90 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.20), residues: 1951 helix: 1.95 (0.18), residues: 862 sheet: -0.24 (0.34), residues: 261 loop : -0.44 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 169 HIS 0.003 0.001 HIS F 227 PHE 0.012 0.001 PHE C 157 TYR 0.013 0.001 TYR E 432 ARG 0.004 0.000 ARG F 77 *********************** 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 130 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 6 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8108 (t0) REVERT: C 134 MET cc_start: 0.8898 (tmm) cc_final: 0.8696 (tmm) REVERT: C 143 ASP cc_start: 0.8410 (m-30) cc_final: 0.8029 (t0) REVERT: F 233 MET cc_start: 0.7719 (mtm) cc_final: 0.7480 (mtp) REVERT: F 403 MET cc_start: 0.7477 (tpp) cc_final: 0.7079 (mmm) REVERT: F 406 MET cc_start: 0.7683 (ppp) cc_final: 0.7248 (ppp) outliers start: 10 outliers final: 6 residues processed: 125 average time/residue: 0.2671 time to fit residues: 52.9248 Evaluate side-chains 121 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain C residue 6 ASP 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 F residue 113 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 5.9990 chunk 174 optimal weight: 0.7980 chunk 179 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 157 optimal weight: 8.9990 chunk 164 optimal weight: 0.8980 chunk 173 optimal weight: 0.0770 chunk 114 optimal weight: 7.9990 overall best weight: 1.7542 ------------------------------------------------------------------------------- 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 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15863 Z= 0.236 Angle : 0.567 11.895 21554 Z= 0.274 Chirality : 0.042 0.146 2362 Planarity : 0.003 0.049 2803 Dihedral : 10.560 170.287 2232 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.66 % Allowed : 13.20 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.20), residues: 1951 helix: 1.96 (0.18), residues: 865 sheet: -0.34 (0.33), residues: 266 loop : -0.38 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 21 HIS 0.004 0.001 HIS E 8 PHE 0.015 0.001 PHE E 149 TYR 0.012 0.001 TYR E 432 ARG 0.005 0.000 ARG F 77 *********************** 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 124 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 6 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8178 (t0) REVERT: C 134 MET cc_start: 0.8933 (tmm) cc_final: 0.8729 (tmm) REVERT: C 143 ASP cc_start: 0.8462 (m-30) cc_final: 0.8087 (t0) REVERT: D 257 MET cc_start: 0.8504 (mmm) cc_final: 0.8245 (mmm) REVERT: F 233 MET cc_start: 0.7721 (mtm) cc_final: 0.7444 (mtm) REVERT: F 403 MET cc_start: 0.7604 (tpp) cc_final: 0.7310 (mmm) REVERT: F 406 MET cc_start: 0.7621 (ppp) cc_final: 0.7230 (ppp) outliers start: 11 outliers final: 9 residues processed: 116 average time/residue: 0.2649 time to fit residues: 48.3863 Evaluate side-chains 120 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 141 PHE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 184 optimal weight: 0.0770 chunk 112 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 chunk 193 optimal weight: 9.9990 chunk 177 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- 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 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15863 Z= 0.160 Angle : 0.550 11.789 21554 Z= 0.262 Chirality : 0.041 0.143 2362 Planarity : 0.003 0.050 2803 Dihedral : 10.509 167.493 2232 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.78 % Allowed : 13.38 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.20), residues: 1951 helix: 1.95 (0.18), residues: 865 sheet: -0.18 (0.34), residues: 251 loop : -0.41 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 169 HIS 0.003 0.001 HIS E 8 PHE 0.020 0.001 PHE B 255 TYR 0.013 0.001 TYR E 432 ARG 0.004 0.000 ARG F 77 ********************** 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 127 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 6 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8155 (t0) REVERT: C 134 MET cc_start: 0.8928 (tmm) cc_final: 0.8706 (tmm) REVERT: C 143 ASP cc_start: 0.8409 (m-30) cc_final: 0.8033 (t0) REVERT: C 159 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8261 (mm-30) REVERT: D 257 MET cc_start: 0.8405 (mmm) cc_final: 0.8177 (mmm) REVERT: F 233 MET cc_start: 0.7714 (mtm) cc_final: 0.7461 (mtm) REVERT: F 406 MET cc_start: 0.7676 (ppp) cc_final: 0.7331 (ppp) outliers start: 13 outliers final: 8 residues processed: 119 average time/residue: 0.2645 time to fit residues: 49.4377 Evaluate side-chains 119 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 141 PHE 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 E residue 145 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 135 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 220 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 = 0.3198 r_free = 0.3198 target = 0.043376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.035084 restraints weight = 84656.248| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 4.37 r_work: 0.2760 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15863 Z= 0.171 Angle : 0.566 12.319 21554 Z= 0.271 Chirality : 0.041 0.140 2362 Planarity : 0.003 0.050 2803 Dihedral : 10.472 167.043 2232 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.60 % Allowed : 13.62 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.20), residues: 1951 helix: 1.94 (0.18), residues: 864 sheet: -0.17 (0.34), residues: 251 loop : -0.42 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 169 HIS 0.003 0.001 HIS C 64 PHE 0.012 0.001 PHE E 149 TYR 0.013 0.001 TYR E 432 ARG 0.004 0.000 ARG F 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2676.00 seconds wall clock time: 50 minutes 41.90 seconds (3041.90 seconds total)