Starting phenix.real_space_refine on Mon Oct 14 05:12:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utq_42546/10_2024/8utq_42546.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utq_42546/10_2024/8utq_42546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utq_42546/10_2024/8utq_42546.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utq_42546/10_2024/8utq_42546.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utq_42546/10_2024/8utq_42546.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utq_42546/10_2024/8utq_42546.cif" } resolution = 3.1 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= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 3 5.21 5 S 114 5.16 5 C 10539 2.51 5 N 2871 2.21 5 O 3285 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 16825 Number of models: 1 Model: "" Number of chains: 12 Chain: "K" Number of atoms: 2911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2911 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 13, 'TRANS': 356} Chain: "A" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3437 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain: "B" Number of atoms: 3381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3381 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain: "E" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3437 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain: "I" Number of atoms: 3381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3381 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.54, per 1000 atoms: 0.69 Number of scatterers: 16825 At special positions: 0 Unit cell: (72.584, 111.408, 198.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 114 16.00 P 13 15.00 Mg 3 11.99 O 3285 8.00 N 2871 7.00 C 10539 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: 4.49 Conformation dependent library (CDL) restraints added in 2.3 seconds 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3918 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 15 sheets defined 50.5% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'K' and resid 16 through 22 removed outlier: 3.761A pdb=" N ARG K 22 " --> pdb=" O ARG K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 77 Processing helix chain 'K' and resid 77 through 86 Processing helix chain 'K' and resid 102 through 108 removed outlier: 4.029A pdb=" N THR K 106 " --> pdb=" O GLY K 102 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET K 107 " --> pdb=" O LYS K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 133 Processing helix chain 'K' and resid 188 through 203 removed outlier: 3.580A pdb=" N ILE K 192 " --> pdb=" O SER K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 254 through 259 Processing helix chain 'K' and resid 262 through 295 removed outlier: 3.696A pdb=" N ALA K 286 " --> pdb=" O ILE K 282 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU K 287 " --> pdb=" O SER K 283 " (cutoff:3.500A) Proline residue: K 292 - end of helix Processing helix chain 'K' and resid 309 through 315 Processing helix chain 'K' and resid 315 through 320 removed outlier: 3.881A pdb=" N GLY K 320 " --> pdb=" O ARG K 316 " (cutoff:3.500A) Processing helix chain 'K' and resid 337 through 350 Processing helix chain 'K' and resid 363 through 373 removed outlier: 3.526A pdb=" N ILE K 369 " --> pdb=" O ASN K 365 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG K 370 " --> pdb=" O ASN K 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 71 through 80 removed outlier: 4.195A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 114 through 129 Processing helix chain 'A' and resid 143 through 161 removed outlier: 3.662A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.587A pdb=" N THR A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 223 through 240 removed outlier: 3.681A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 251 through 258 removed outlier: 3.651A pdb=" N ASN A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.040A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.848A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.940A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.012A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 436 removed outlier: 4.113A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY A 436 " --> pdb=" O TYR A 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 46 through 49 Processing helix chain 'B' and resid 69 through 78 removed outlier: 4.228A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.582A pdb=" N PHE B 85 " --> pdb=" O GLY B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 107 through 127 removed outlier: 4.182A pdb=" N GLU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N CYS B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 removed outlier: 3.735A pdb=" N SER B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 193 removed outlier: 3.634A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.584A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 241 Processing helix chain 'B' and resid 249 through 258 removed outlier: 3.582A pdb=" N LEU B 253 " --> pdb=" O ASP B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.692A pdb=" N PHE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 373 through 390 removed outlier: 4.205A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 4.045A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 426 removed outlier: 3.738A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN B 426 " --> pdb=" O TYR B 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 29 Processing helix chain 'E' and resid 36 through 43 removed outlier: 3.850A pdb=" N LYS E 40 " --> pdb=" O MET E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 80 removed outlier: 4.260A pdb=" N ILE E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 114 through 129 removed outlier: 3.571A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 161 removed outlier: 4.154A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 197 removed outlier: 4.890A pdb=" N HIS E 192 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 216 Processing helix chain 'E' and resid 223 through 240 removed outlier: 3.851A pdb=" N LEU E 227 " --> pdb=" O THR E 223 " (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: 4.078A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.804A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 338 removed outlier: 3.564A pdb=" N VAL E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS E 338 " --> pdb=" O THR E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 400 removed outlier: 4.057A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 3.829A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 436 removed outlier: 4.358A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 29 Processing helix chain 'I' and resid 46 through 49 Processing helix chain 'I' and resid 69 through 78 removed outlier: 4.275A pdb=" N MET I 73 " --> pdb=" O GLU I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.530A pdb=" N PHE I 85 " --> pdb=" O GLY I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 88 No H-bonds generated for 'chain 'I' and resid 86 through 88' Processing helix chain 'I' and resid 100 through 106 Processing helix chain 'I' and resid 108 through 127 removed outlier: 3.682A pdb=" N LEU I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER I 126 " --> pdb=" O LYS I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 159 removed outlier: 3.625A pdb=" N SER I 145 " --> pdb=" O GLY I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 196 removed outlier: 3.594A pdb=" N ASN I 184 " --> pdb=" O VAL I 180 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN I 191 " --> pdb=" O LEU I 187 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU I 194 " --> pdb=" O HIS I 190 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 214 Processing helix chain 'I' and resid 221 through 237 removed outlier: 3.540A pdb=" N LEU I 225 " --> pdb=" O THR I 221 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR I 237 " --> pdb=" O MET I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 241 Processing helix chain 'I' and resid 249 through 258 Processing helix chain 'I' and resid 275 through 280 removed outlier: 3.528A pdb=" N SER I 278 " --> pdb=" O SER I 275 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLN I 280 " --> pdb=" O GLY I 277 " (cutoff:3.500A) Processing helix chain 'I' and resid 285 through 295 Processing helix chain 'I' and resid 304 through 308 Processing helix chain 'I' and resid 322 through 337 removed outlier: 3.568A pdb=" N VAL I 326 " --> pdb=" O SER I 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 341 Processing helix chain 'I' and resid 373 through 390 removed outlier: 4.292A pdb=" N LEU I 377 " --> pdb=" O ALA I 373 " (cutoff:3.500A) Processing helix chain 'I' and resid 394 through 400 removed outlier: 4.091A pdb=" N TYR I 398 " --> pdb=" O PHE I 394 " (cutoff:3.500A) Processing helix chain 'I' and resid 404 through 424 removed outlier: 3.782A pdb=" N PHE I 408 " --> pdb=" O ASP I 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 56 through 57 removed outlier: 5.436A pdb=" N ASN K 90 " --> pdb=" O ARG K 324 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ALA K 326 " --> pdb=" O ASN K 90 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N CYS K 92 " --> pdb=" O ALA K 326 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL K 328 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N PHE K 94 " --> pdb=" O VAL K 328 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ALA K 330 " --> pdb=" O PHE K 94 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N TYR K 96 " --> pdb=" O ALA K 330 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL K 91 " --> pdb=" O SER K 245 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N VAL K 247 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE K 93 " --> pdb=" O VAL K 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 56 through 57 removed outlier: 5.436A pdb=" N ASN K 90 " --> pdb=" O ARG K 324 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ALA K 326 " --> pdb=" O ASN K 90 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N CYS K 92 " --> pdb=" O ALA K 326 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL K 328 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N PHE K 94 " --> pdb=" O VAL K 328 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ALA K 330 " --> pdb=" O PHE K 94 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N TYR K 96 " --> pdb=" O ALA K 330 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL K 91 " --> pdb=" O SER K 245 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N VAL K 247 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE K 93 " --> pdb=" O VAL K 247 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL K 142 " --> pdb=" O VAL K 186 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 28 through 31 Processing sheet with id=AA4, first strand: chain 'K' and resid 168 through 171 Processing sheet with id=AA5, first strand: chain 'K' and resid 205 through 206 Processing sheet with id=AA6, first strand: chain 'A' and resid 65 through 68 removed outlier: 7.356A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA8, first strand: chain 'A' and resid 269 through 272 Processing sheet with id=AA9, first strand: chain 'B' and resid 90 through 91 removed outlier: 8.137A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ALA B 9 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS B 137 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N ASP B 203 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 12.130A pdb=" N PHE B 270 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N LYS B 350 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL B 313 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ALA B 352 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA B 315 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N CYS B 354 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHE B 317 " --> pdb=" O CYS B 354 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AB2, first strand: chain 'E' and resid 65 through 68 removed outlier: 7.684A pdb=" N GLU E 3 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N PHE E 135 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE E 5 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VAL E 137 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE E 7 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N HIS E 139 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL E 9 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER E 165 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE E 171 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER E 170 " --> pdb=" O VAL E 204 " (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 269 through 272 Processing sheet with id=AB5, first strand: chain 'I' and resid 90 through 92 removed outlier: 5.948A pdb=" N LEU I 65 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N HIS I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALA I 9 " --> pdb=" O HIS I 137 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS I 137 " --> pdb=" O PHE I 167 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N TYR I 200 " --> pdb=" O MET I 164 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR I 166 " --> pdb=" O TYR I 200 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ILE I 202 " --> pdb=" O THR I 166 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N SER I 168 " --> pdb=" O ILE I 202 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N PHE I 265 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N SER I 371 " --> pdb=" O PHE I 265 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 51 through 53 812 hydrogen bonds defined for protein. 2316 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: 5.12 Time building geometry restraints manager: 5.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2997 1.32 - 1.45: 4536 1.45 - 1.57: 9451 1.57 - 1.70: 28 1.70 - 1.82: 183 Bond restraints: 17195 Sorted by residual: bond pdb=" O3A ANP K 502 " pdb=" PB ANP K 502 " ideal model delta sigma weight residual 1.700 1.559 0.141 2.00e-02 2.50e+03 5.01e+01 bond pdb=" N3B ANP K 502 " pdb=" PG ANP K 502 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" O5' ANP K 502 " pdb=" PA ANP K 502 " ideal model delta sigma weight residual 1.655 1.582 0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" N VAL K 247 " pdb=" CA VAL K 247 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.14e-02 7.69e+03 9.98e+00 bond pdb=" N VAL B 23 " pdb=" CA VAL B 23 " ideal model delta sigma weight residual 1.461 1.493 -0.031 1.17e-02 7.31e+03 7.21e+00 ... (remaining 17190 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.34: 23088 3.34 - 6.68: 253 6.68 - 10.03: 11 10.03 - 13.37: 4 13.37 - 16.71: 1 Bond angle restraints: 23357 Sorted by residual: angle pdb=" PB ANP K 502 " pdb=" N3B ANP K 502 " pdb=" PG ANP K 502 " ideal model delta sigma weight residual 126.95 110.24 16.71 3.00e+00 1.11e-01 3.10e+01 angle pdb=" C ALA K 358 " pdb=" N VAL K 359 " pdb=" CA VAL K 359 " ideal model delta sigma weight residual 121.97 131.56 -9.59 1.80e+00 3.09e-01 2.84e+01 angle pdb=" CA GLN I 426 " pdb=" CB GLN I 426 " pdb=" CG GLN I 426 " ideal model delta sigma weight residual 114.10 122.02 -7.92 2.00e+00 2.50e-01 1.57e+01 angle pdb=" C19 TA1 B 502 " pdb=" C18 TA1 B 502 " pdb=" C20 TA1 B 502 " ideal model delta sigma weight residual 112.17 100.71 11.46 3.00e+00 1.11e-01 1.46e+01 angle pdb=" O1B ANP K 502 " pdb=" PB ANP K 502 " pdb=" O2B ANP K 502 " ideal model delta sigma weight residual 120.08 108.74 11.34 3.00e+00 1.11e-01 1.43e+01 ... (remaining 23352 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 10080 35.29 - 70.58: 293 70.58 - 105.87: 56 105.87 - 141.15: 19 141.15 - 176.44: 6 Dihedral angle restraints: 10454 sinusoidal: 4348 harmonic: 6106 Sorted by residual: dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -107.17 176.44 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -43.61 148.20 1 2.00e+01 2.50e-03 4.44e+01 dihedral pdb=" C8 GTP E 501 " pdb=" C1' GTP E 501 " pdb=" N9 GTP E 501 " pdb=" O4' GTP E 501 " ideal model delta sinusoidal sigma weight residual 104.59 -33.38 137.97 1 2.00e+01 2.50e-03 4.18e+01 ... (remaining 10451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2424 0.105 - 0.210: 133 0.210 - 0.315: 2 0.315 - 0.420: 0 0.420 - 0.526: 1 Chirality restraints: 2560 Sorted by residual: chirality pdb=" C18 TA1 B 502 " pdb=" C10 TA1 B 502 " pdb=" C17 TA1 B 502 " pdb=" C20 TA1 B 502 " both_signs ideal model delta sigma weight residual False -3.16 -2.64 -0.53 2.00e-01 2.50e+01 6.90e+00 chirality pdb=" C3' ANP K 502 " pdb=" C2' ANP K 502 " pdb=" C4' ANP K 502 " pdb=" O3' ANP K 502 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C02 TA1 B 502 " pdb=" C01 TA1 B 502 " pdb=" C10 TA1 B 502 " pdb=" O02 TA1 B 502 " both_signs ideal model delta sigma weight residual False 2.56 2.79 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 2557 not shown) Planarity restraints: 3030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY K 291 " 0.065 5.00e-02 4.00e+02 9.73e-02 1.52e+01 pdb=" N PRO K 292 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO K 292 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO K 292 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 21 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.47e+00 pdb=" C TRP B 21 " -0.047 2.00e-02 2.50e+03 pdb=" O TRP B 21 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU B 22 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN K 39 " -0.041 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO K 40 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO K 40 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO K 40 " -0.035 5.00e-02 4.00e+02 ... (remaining 3027 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 94 2.49 - 3.09: 12325 3.09 - 3.70: 25001 3.70 - 4.30: 36346 4.30 - 4.90: 62751 Nonbonded interactions: 136517 Sorted by model distance: nonbonded pdb=" O3B GTP A 501 " pdb="MG MG A 502 " model vdw 1.891 2.170 nonbonded pdb=" O1A GTP A 501 " pdb="MG MG A 502 " model vdw 1.927 2.170 nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 1.928 2.170 nonbonded pdb="MG MG K 501 " pdb=" O2B ANP K 502 " model vdw 1.967 2.170 nonbonded pdb=" O1G GTP E 501 " pdb="MG MG E 502 " model vdw 1.995 2.170 ... (remaining 136512 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'I' } 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: 3.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.760 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 39.850 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.080 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 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 : 0.005 0.141 17195 Z= 0.326 Angle : 0.808 16.710 23357 Z= 0.422 Chirality : 0.048 0.526 2560 Planarity : 0.006 0.097 3030 Dihedral : 18.598 176.442 6536 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.10 % Favored : 95.76 % Rotamer: Outliers : 0.22 % Allowed : 12.43 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 0.10 (0.18), residues: 2100 helix: 1.19 (0.18), residues: 870 sheet: -0.28 (0.27), residues: 357 loop : -0.89 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 57 HIS 0.003 0.001 HIS A 266 PHE 0.015 0.001 PHE E 255 TYR 0.022 0.001 TYR I 422 ARG 0.014 0.001 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 297 time to evaluate : 2.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 13 ARG cc_start: 0.7260 (ptm-80) cc_final: 0.7031 (ptt-90) REVERT: K 50 PHE cc_start: 0.7233 (m-80) cc_final: 0.6660 (m-80) REVERT: K 138 MET cc_start: 0.5055 (mtp) cc_final: 0.4839 (pmm) REVERT: B 291 GLN cc_start: 0.8103 (tp-100) cc_final: 0.7860 (tp-100) REVERT: I 31 ASP cc_start: 0.8155 (t70) cc_final: 0.7704 (t70) outliers start: 4 outliers final: 3 residues processed: 300 average time/residue: 0.3133 time to fit residues: 139.9992 Evaluate side-chains 281 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 278 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 386 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 178 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 165 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 191 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 90 ASN K 366 ASN A 107 HIS B 37 HIS B 204 ASN E 61 HIS E 107 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17195 Z= 0.276 Angle : 0.627 10.776 23357 Z= 0.310 Chirality : 0.046 0.316 2560 Planarity : 0.005 0.093 3030 Dihedral : 13.762 174.177 2600 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.52 % Favored : 96.33 % Rotamer: Outliers : 1.66 % Allowed : 11.66 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 0.67 (0.19), residues: 2100 helix: 1.77 (0.18), residues: 881 sheet: 0.07 (0.27), residues: 353 loop : -0.77 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 21 HIS 0.004 0.001 HIS E 192 PHE 0.027 0.001 PHE K 225 TYR 0.013 0.001 TYR B 50 ARG 0.007 0.001 ARG I 380 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 297 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 50 PHE cc_start: 0.7307 (m-80) cc_final: 0.6798 (m-80) REVERT: K 359 VAL cc_start: 0.1926 (OUTLIER) cc_final: 0.1370 (p) REVERT: A 3 GLU cc_start: 0.7303 (pt0) cc_final: 0.6880 (pt0) REVERT: A 218 ASP cc_start: 0.8630 (t0) cc_final: 0.8291 (t70) REVERT: A 308 ARG cc_start: 0.8755 (mtm-85) cc_final: 0.8530 (mtm-85) REVERT: E 62 VAL cc_start: 0.9267 (t) cc_final: 0.9038 (m) REVERT: E 127 ASP cc_start: 0.8525 (m-30) cc_final: 0.8298 (m-30) REVERT: E 322 ASP cc_start: 0.8228 (t0) cc_final: 0.8018 (t0) REVERT: I 31 ASP cc_start: 0.8263 (t70) cc_final: 0.7893 (t70) REVERT: I 67 ASP cc_start: 0.8288 (t0) cc_final: 0.8054 (t0) REVERT: I 295 ASP cc_start: 0.8617 (t0) cc_final: 0.8234 (t0) REVERT: I 297 LYS cc_start: 0.8967 (mtmm) cc_final: 0.8766 (mtmm) REVERT: I 426 GLN cc_start: 0.8584 (tm-30) cc_final: 0.8348 (tt0) outliers start: 30 outliers final: 14 residues processed: 314 average time/residue: 0.3141 time to fit residues: 149.4643 Evaluate side-chains 289 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 274 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 243 LYS Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 359 VAL Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain I residue 172 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 106 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 159 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 191 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 153 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17195 Z= 0.193 Angle : 0.563 8.999 23357 Z= 0.278 Chirality : 0.045 0.464 2560 Planarity : 0.004 0.086 3030 Dihedral : 9.744 173.460 2595 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.57 % Favored : 96.29 % Rotamer: Outliers : 1.71 % Allowed : 11.77 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 0.88 (0.19), residues: 2100 helix: 1.90 (0.18), residues: 907 sheet: 0.11 (0.28), residues: 364 loop : -0.65 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 21 HIS 0.003 0.001 HIS E 192 PHE 0.018 0.001 PHE K 225 TYR 0.015 0.001 TYR K 140 ARG 0.009 0.000 ARG K 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 322 time to evaluate : 2.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 30 MET cc_start: 0.7416 (tmm) cc_final: 0.6781 (ptp) REVERT: K 359 VAL cc_start: 0.1593 (OUTLIER) cc_final: 0.0883 (p) REVERT: A 3 GLU cc_start: 0.7184 (pt0) cc_final: 0.6766 (pt0) REVERT: A 218 ASP cc_start: 0.8639 (t0) cc_final: 0.8316 (t70) REVERT: B 12 CYS cc_start: 0.8194 (t) cc_final: 0.7993 (t) REVERT: B 213 ARG cc_start: 0.8414 (tpp80) cc_final: 0.7951 (mtm-85) REVERT: B 257 MET cc_start: 0.8276 (mmm) cc_final: 0.7950 (mmm) REVERT: E 127 ASP cc_start: 0.8504 (m-30) cc_final: 0.8294 (m-30) REVERT: E 434 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7182 (mm-30) REVERT: I 31 ASP cc_start: 0.8256 (t70) cc_final: 0.7843 (t70) REVERT: I 67 ASP cc_start: 0.8373 (t0) cc_final: 0.8065 (t0) REVERT: I 295 ASP cc_start: 0.8613 (t0) cc_final: 0.8162 (t0) REVERT: I 297 LYS cc_start: 0.8968 (mtmm) cc_final: 0.8714 (mtmm) REVERT: I 376 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7767 (mm-30) REVERT: I 426 GLN cc_start: 0.8596 (tm-30) cc_final: 0.8163 (tm-30) outliers start: 31 outliers final: 14 residues processed: 335 average time/residue: 0.2902 time to fit residues: 147.8672 Evaluate side-chains 301 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 286 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 243 LYS Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 359 VAL Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain I residue 377 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 189 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 192 optimal weight: 0.7980 chunk 203 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 182 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17195 Z= 0.269 Angle : 0.575 8.402 23357 Z= 0.290 Chirality : 0.045 0.335 2560 Planarity : 0.004 0.082 3030 Dihedral : 9.168 173.830 2595 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.00 % Favored : 95.90 % Rotamer: Outliers : 1.66 % Allowed : 13.31 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 0.87 (0.19), residues: 2100 helix: 1.90 (0.18), residues: 906 sheet: 0.16 (0.28), residues: 363 loop : -0.69 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 21 HIS 0.005 0.001 HIS I 137 PHE 0.025 0.001 PHE K 225 TYR 0.014 0.001 TYR K 146 ARG 0.006 0.000 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 291 time to evaluate : 2.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 30 MET cc_start: 0.7498 (tmm) cc_final: 0.6516 (ptp) REVERT: K 54 TYR cc_start: 0.6467 (OUTLIER) cc_final: 0.6202 (m-80) REVERT: K 105 TYR cc_start: 0.7752 (t80) cc_final: 0.7261 (t80) REVERT: A 121 ARG cc_start: 0.6596 (tpt-90) cc_final: 0.6331 (tpt-90) REVERT: A 203 MET cc_start: 0.8754 (mtt) cc_final: 0.8513 (mtt) REVERT: B 12 CYS cc_start: 0.8352 (t) cc_final: 0.8132 (t) REVERT: B 257 MET cc_start: 0.8316 (mmm) cc_final: 0.7930 (mmm) REVERT: B 291 GLN cc_start: 0.8055 (tp-100) cc_final: 0.7730 (tp-100) REVERT: E 127 ASP cc_start: 0.8522 (m-30) cc_final: 0.8301 (m-30) REVERT: E 434 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7225 (mm-30) REVERT: I 31 ASP cc_start: 0.8274 (t70) cc_final: 0.7900 (t70) REVERT: I 67 ASP cc_start: 0.8435 (t0) cc_final: 0.8120 (t0) REVERT: I 295 ASP cc_start: 0.8624 (t0) cc_final: 0.8139 (t0) REVERT: I 297 LYS cc_start: 0.8973 (mtmm) cc_final: 0.8718 (mtmm) REVERT: I 312 THR cc_start: 0.8825 (m) cc_final: 0.8613 (p) REVERT: I 426 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8186 (tm-30) outliers start: 30 outliers final: 19 residues processed: 305 average time/residue: 0.2954 time to fit residues: 135.6013 Evaluate side-chains 301 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 281 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 54 TYR Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 359 VAL Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain I residue 188 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 169 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 84 optimal weight: 0.0470 chunk 174 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 104 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN K 337 ASN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17195 Z= 0.272 Angle : 0.574 8.245 23357 Z= 0.289 Chirality : 0.045 0.282 2560 Planarity : 0.004 0.080 3030 Dihedral : 9.085 173.315 2595 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.19 % Favored : 95.76 % Rotamer: Outliers : 2.10 % Allowed : 13.37 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 0.87 (0.19), residues: 2100 helix: 1.97 (0.17), residues: 902 sheet: 0.02 (0.28), residues: 372 loop : -0.69 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 21 HIS 0.004 0.001 HIS A 283 PHE 0.029 0.001 PHE K 225 TYR 0.014 0.001 TYR K 140 ARG 0.006 0.000 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 291 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 5 SER cc_start: 0.4539 (OUTLIER) cc_final: 0.4043 (p) REVERT: K 30 MET cc_start: 0.7522 (tmm) cc_final: 0.6502 (ptp) REVERT: K 50 PHE cc_start: 0.7518 (m-80) cc_final: 0.6833 (m-80) REVERT: K 107 MET cc_start: 0.7336 (mmp) cc_final: 0.7053 (mmp) REVERT: K 159 ASN cc_start: 0.8908 (OUTLIER) cc_final: 0.8414 (t0) REVERT: K 209 ASN cc_start: 0.8332 (t0) cc_final: 0.8096 (t0) REVERT: A 121 ARG cc_start: 0.6593 (tpt-90) cc_final: 0.6342 (tpt-90) REVERT: B 12 CYS cc_start: 0.8369 (t) cc_final: 0.8143 (t) REVERT: B 213 ARG cc_start: 0.8415 (tpp80) cc_final: 0.7932 (mtm-85) REVERT: B 257 MET cc_start: 0.8291 (mmm) cc_final: 0.7931 (mmm) REVERT: B 291 GLN cc_start: 0.8132 (tp-100) cc_final: 0.7753 (tp-100) REVERT: E 127 ASP cc_start: 0.8519 (m-30) cc_final: 0.8295 (m-30) REVERT: E 154 MET cc_start: 0.8592 (mmm) cc_final: 0.8109 (mmm) REVERT: E 168 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7974 (mm-30) REVERT: E 434 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7272 (mm-30) REVERT: I 31 ASP cc_start: 0.8277 (t70) cc_final: 0.7901 (t70) REVERT: I 67 ASP cc_start: 0.8451 (t0) cc_final: 0.8124 (t0) REVERT: I 295 ASP cc_start: 0.8622 (t0) cc_final: 0.8120 (t0) REVERT: I 297 LYS cc_start: 0.9003 (mtmm) cc_final: 0.8740 (mtmm) REVERT: I 312 THR cc_start: 0.8836 (m) cc_final: 0.8603 (p) REVERT: I 426 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8269 (tm-30) outliers start: 38 outliers final: 20 residues processed: 315 average time/residue: 0.2947 time to fit residues: 138.5278 Evaluate side-chains 300 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 277 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 159 ASN Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain E residue 2 ARG Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain I residue 139 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 68 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 42 GLN K 159 ASN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 334 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17195 Z= 0.220 Angle : 0.563 8.578 23357 Z= 0.282 Chirality : 0.044 0.258 2560 Planarity : 0.004 0.078 3030 Dihedral : 8.977 172.373 2595 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.00 % Favored : 95.95 % Rotamer: Outliers : 1.88 % Allowed : 14.09 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 0.94 (0.19), residues: 2100 helix: 2.05 (0.18), residues: 901 sheet: 0.03 (0.27), residues: 372 loop : -0.68 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 21 HIS 0.003 0.001 HIS A 283 PHE 0.026 0.001 PHE K 225 TYR 0.016 0.001 TYR K 54 ARG 0.009 0.000 ARG K 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 292 time to evaluate : 2.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 30 MET cc_start: 0.7494 (tmm) cc_final: 0.6499 (ptp) REVERT: K 50 PHE cc_start: 0.7504 (m-80) cc_final: 0.6827 (m-80) REVERT: K 76 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7858 (p0) REVERT: K 107 MET cc_start: 0.7443 (mmp) cc_final: 0.7086 (mmp) REVERT: K 159 ASN cc_start: 0.8816 (OUTLIER) cc_final: 0.8279 (t0) REVERT: K 209 ASN cc_start: 0.8319 (t0) cc_final: 0.8108 (t0) REVERT: A 121 ARG cc_start: 0.6515 (tpt-90) cc_final: 0.6284 (tpt-90) REVERT: B 12 CYS cc_start: 0.8320 (t) cc_final: 0.8091 (t) REVERT: B 213 ARG cc_start: 0.8398 (tpp80) cc_final: 0.8026 (mtm-85) REVERT: B 257 MET cc_start: 0.8244 (mmm) cc_final: 0.7875 (mmm) REVERT: B 291 GLN cc_start: 0.8135 (tp-100) cc_final: 0.7769 (tp-100) REVERT: E 127 ASP cc_start: 0.8504 (m-30) cc_final: 0.8291 (m-30) REVERT: E 434 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7269 (mm-30) REVERT: I 31 ASP cc_start: 0.8270 (t70) cc_final: 0.7882 (t70) REVERT: I 67 ASP cc_start: 0.8450 (t0) cc_final: 0.8106 (t0) REVERT: I 295 ASP cc_start: 0.8610 (t0) cc_final: 0.8094 (t0) REVERT: I 297 LYS cc_start: 0.8993 (mtmm) cc_final: 0.8725 (mtmm) REVERT: I 312 THR cc_start: 0.8821 (m) cc_final: 0.8593 (p) REVERT: I 426 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8271 (tm-30) outliers start: 34 outliers final: 25 residues processed: 314 average time/residue: 0.3016 time to fit residues: 141.9494 Evaluate side-chains 308 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 281 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 159 ASN Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 196 MET Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 308 ASP Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain E residue 2 ARG Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 172 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 196 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 171 optimal weight: 0.0870 chunk 113 optimal weight: 3.9990 chunk 203 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17195 Z= 0.273 Angle : 0.583 8.907 23357 Z= 0.294 Chirality : 0.045 0.240 2560 Planarity : 0.004 0.078 3030 Dihedral : 8.995 172.274 2595 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.00 % Favored : 95.95 % Rotamer: Outliers : 1.99 % Allowed : 14.70 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 0.90 (0.19), residues: 2100 helix: 2.02 (0.18), residues: 901 sheet: 0.02 (0.27), residues: 372 loop : -0.70 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 388 HIS 0.004 0.001 HIS I 137 PHE 0.024 0.001 PHE K 225 TYR 0.015 0.001 TYR K 140 ARG 0.008 0.000 ARG K 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 287 time to evaluate : 1.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 30 MET cc_start: 0.7463 (tmm) cc_final: 0.6606 (mtt) REVERT: K 50 PHE cc_start: 0.7590 (m-80) cc_final: 0.6914 (m-80) REVERT: K 76 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7890 (p0) REVERT: K 107 MET cc_start: 0.7562 (mmp) cc_final: 0.7162 (mmp) REVERT: K 116 GLN cc_start: 0.7443 (pm20) cc_final: 0.6837 (pm20) REVERT: K 159 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8277 (t0) REVERT: K 209 ASN cc_start: 0.8346 (t0) cc_final: 0.8115 (t0) REVERT: A 203 MET cc_start: 0.8779 (mtt) cc_final: 0.8490 (mtt) REVERT: B 213 ARG cc_start: 0.8406 (tpp80) cc_final: 0.7940 (mtm-85) REVERT: B 257 MET cc_start: 0.8268 (mmm) cc_final: 0.7887 (mmm) REVERT: B 291 GLN cc_start: 0.8152 (tp-100) cc_final: 0.7767 (tp-100) REVERT: E 127 ASP cc_start: 0.8513 (m-30) cc_final: 0.8302 (m-30) REVERT: E 154 MET cc_start: 0.8624 (mmm) cc_final: 0.8141 (mmm) REVERT: E 168 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7995 (mm-30) REVERT: E 434 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7267 (mm-30) REVERT: I 31 ASP cc_start: 0.8292 (t70) cc_final: 0.7925 (t70) REVERT: I 67 ASP cc_start: 0.8443 (t0) cc_final: 0.8087 (t0) REVERT: I 147 MET cc_start: 0.8506 (mtp) cc_final: 0.8134 (ttm) REVERT: I 295 ASP cc_start: 0.8619 (t0) cc_final: 0.8098 (t0) REVERT: I 297 LYS cc_start: 0.8999 (mtmm) cc_final: 0.8724 (mtmm) REVERT: I 312 THR cc_start: 0.8830 (m) cc_final: 0.8586 (p) REVERT: I 426 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8280 (tm-30) outliers start: 36 outliers final: 26 residues processed: 311 average time/residue: 0.3038 time to fit residues: 140.2741 Evaluate side-chains 311 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 282 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 159 ASN Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 196 MET Chi-restraints excluded: chain K residue 215 SER Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain E residue 2 ARG Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain I residue 139 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 125 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 129 optimal weight: 0.0010 chunk 138 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17195 Z= 0.220 Angle : 0.574 9.170 23357 Z= 0.288 Chirality : 0.044 0.225 2560 Planarity : 0.004 0.077 3030 Dihedral : 8.926 171.439 2595 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.93 % Allowed : 14.59 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 0.95 (0.19), residues: 2100 helix: 2.07 (0.18), residues: 899 sheet: 0.02 (0.27), residues: 372 loop : -0.68 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 388 HIS 0.004 0.001 HIS I 137 PHE 0.026 0.001 PHE K 86 TYR 0.014 0.001 TYR K 140 ARG 0.009 0.000 ARG K 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 293 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 50 PHE cc_start: 0.7566 (m-80) cc_final: 0.6915 (m-80) REVERT: K 72 GLN cc_start: 0.8918 (tm-30) cc_final: 0.8324 (tm-30) REVERT: K 81 MET cc_start: 0.7331 (tpp) cc_final: 0.6531 (tpp) REVERT: K 90 ASN cc_start: 0.5547 (OUTLIER) cc_final: 0.5335 (p0) REVERT: K 107 MET cc_start: 0.7650 (mmp) cc_final: 0.7263 (mmp) REVERT: K 159 ASN cc_start: 0.8817 (OUTLIER) cc_final: 0.8276 (t0) REVERT: K 209 ASN cc_start: 0.8364 (t0) cc_final: 0.8146 (t0) REVERT: A 203 MET cc_start: 0.8774 (mtt) cc_final: 0.8505 (mtt) REVERT: B 12 CYS cc_start: 0.8331 (t) cc_final: 0.8093 (t) REVERT: B 213 ARG cc_start: 0.8396 (tpp80) cc_final: 0.8029 (mtm-85) REVERT: B 257 MET cc_start: 0.8221 (mmm) cc_final: 0.7842 (mmm) REVERT: B 291 GLN cc_start: 0.8133 (tp-100) cc_final: 0.7736 (tp-100) REVERT: E 127 ASP cc_start: 0.8506 (m-30) cc_final: 0.8297 (m-30) REVERT: E 154 MET cc_start: 0.8610 (mmm) cc_final: 0.8077 (mmm) REVERT: E 168 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7953 (mm-30) REVERT: E 245 ASP cc_start: 0.7855 (p0) cc_final: 0.7490 (p0) REVERT: E 434 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7325 (mm-30) REVERT: I 31 ASP cc_start: 0.8287 (t70) cc_final: 0.7911 (t70) REVERT: I 67 ASP cc_start: 0.8445 (t0) cc_final: 0.8076 (t0) REVERT: I 295 ASP cc_start: 0.8619 (t0) cc_final: 0.8105 (t0) REVERT: I 297 LYS cc_start: 0.8994 (mtmm) cc_final: 0.8715 (mtmm) REVERT: I 312 THR cc_start: 0.8808 (m) cc_final: 0.8569 (p) REVERT: I 426 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8306 (tm-30) outliers start: 35 outliers final: 25 residues processed: 315 average time/residue: 0.2953 time to fit residues: 139.3416 Evaluate side-chains 308 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 280 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 159 ASN Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 196 MET Chi-restraints excluded: chain K residue 215 SER Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain E residue 2 ARG Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 422 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 194 optimal weight: 0.6980 chunk 177 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 179 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN A 28 HIS A 197 HIS A 249 ASN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17195 Z= 0.205 Angle : 0.579 9.331 23357 Z= 0.290 Chirality : 0.044 0.213 2560 Planarity : 0.004 0.076 3030 Dihedral : 8.852 170.693 2595 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.60 % Allowed : 15.03 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 0.99 (0.19), residues: 2100 helix: 2.14 (0.18), residues: 899 sheet: 0.01 (0.27), residues: 372 loop : -0.68 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 21 HIS 0.003 0.001 HIS I 137 PHE 0.024 0.001 PHE K 225 TYR 0.013 0.001 TYR K 140 ARG 0.009 0.000 ARG K 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 297 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 30 MET cc_start: 0.7542 (tmm) cc_final: 0.6086 (mtm) REVERT: K 50 PHE cc_start: 0.7574 (m-80) cc_final: 0.6881 (m-80) REVERT: K 81 MET cc_start: 0.7398 (tpp) cc_final: 0.6532 (tpp) REVERT: K 86 PHE cc_start: 0.7164 (OUTLIER) cc_final: 0.6085 (t80) REVERT: K 107 MET cc_start: 0.7704 (mmp) cc_final: 0.7343 (mmp) REVERT: K 159 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8287 (t0) REVERT: K 209 ASN cc_start: 0.8351 (t0) cc_final: 0.8136 (t0) REVERT: B 12 CYS cc_start: 0.8307 (t) cc_final: 0.8082 (t) REVERT: B 213 ARG cc_start: 0.8436 (tpp80) cc_final: 0.8089 (mtm-85) REVERT: B 257 MET cc_start: 0.8185 (mmm) cc_final: 0.7815 (mmm) REVERT: B 291 GLN cc_start: 0.8135 (tp-100) cc_final: 0.7733 (tp-100) REVERT: E 127 ASP cc_start: 0.8501 (m-30) cc_final: 0.8295 (m-30) REVERT: E 154 MET cc_start: 0.8589 (mmm) cc_final: 0.8037 (mmm) REVERT: E 168 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7945 (mm-30) REVERT: E 434 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7320 (mm-30) REVERT: I 31 ASP cc_start: 0.8284 (t70) cc_final: 0.7898 (t70) REVERT: I 67 ASP cc_start: 0.8430 (t0) cc_final: 0.8052 (t0) REVERT: I 295 ASP cc_start: 0.8619 (t0) cc_final: 0.8096 (t0) REVERT: I 297 LYS cc_start: 0.8987 (mtmm) cc_final: 0.8705 (mtmm) REVERT: I 312 THR cc_start: 0.8808 (m) cc_final: 0.8570 (p) REVERT: I 426 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8307 (tm-30) outliers start: 29 outliers final: 24 residues processed: 316 average time/residue: 0.3063 time to fit residues: 144.2022 Evaluate side-chains 312 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 285 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 159 ASN Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 215 SER Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain E residue 2 ARG Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 422 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 200 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 210 optimal weight: 0.6980 chunk 193 optimal weight: 5.9990 chunk 167 optimal weight: 0.7980 chunk 17 optimal weight: 0.4980 chunk 129 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17195 Z= 0.225 Angle : 0.591 9.894 23357 Z= 0.295 Chirality : 0.044 0.207 2560 Planarity : 0.004 0.076 3030 Dihedral : 8.833 170.289 2595 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.66 % Allowed : 15.30 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 0.97 (0.19), residues: 2100 helix: 2.12 (0.18), residues: 899 sheet: -0.01 (0.27), residues: 372 loop : -0.68 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 344 HIS 0.013 0.001 HIS K 59 PHE 0.025 0.001 PHE K 225 TYR 0.014 0.001 TYR K 140 ARG 0.010 0.000 ARG K 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 289 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 30 MET cc_start: 0.7488 (tmm) cc_final: 0.6036 (mtm) REVERT: K 50 PHE cc_start: 0.7570 (m-80) cc_final: 0.6882 (m-80) REVERT: K 81 MET cc_start: 0.7385 (tpp) cc_final: 0.6532 (tpp) REVERT: K 86 PHE cc_start: 0.7168 (OUTLIER) cc_final: 0.6135 (t80) REVERT: K 107 MET cc_start: 0.7700 (mmp) cc_final: 0.7328 (mmp) REVERT: K 159 ASN cc_start: 0.8810 (OUTLIER) cc_final: 0.8300 (t0) REVERT: K 209 ASN cc_start: 0.8360 (t0) cc_final: 0.8152 (t0) REVERT: B 12 CYS cc_start: 0.8327 (t) cc_final: 0.8094 (t) REVERT: B 213 ARG cc_start: 0.8390 (tpp80) cc_final: 0.8033 (mtm-85) REVERT: B 257 MET cc_start: 0.8199 (mmm) cc_final: 0.7826 (mmm) REVERT: B 291 GLN cc_start: 0.8135 (tp-100) cc_final: 0.7728 (tp-100) REVERT: E 127 ASP cc_start: 0.8503 (m-30) cc_final: 0.8300 (m-30) REVERT: E 154 MET cc_start: 0.8600 (mmm) cc_final: 0.8025 (mmm) REVERT: E 168 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7942 (mm-30) REVERT: E 434 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7330 (mm-30) REVERT: I 31 ASP cc_start: 0.8290 (t70) cc_final: 0.7917 (t70) REVERT: I 67 ASP cc_start: 0.8444 (t0) cc_final: 0.8076 (t0) REVERT: I 295 ASP cc_start: 0.8620 (t0) cc_final: 0.8093 (t0) REVERT: I 297 LYS cc_start: 0.8991 (mtmm) cc_final: 0.8705 (mtmm) REVERT: I 300 MET cc_start: 0.8620 (mtm) cc_final: 0.8382 (mtm) REVERT: I 312 THR cc_start: 0.8814 (m) cc_final: 0.8568 (p) REVERT: I 426 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8314 (tm-30) outliers start: 30 outliers final: 25 residues processed: 308 average time/residue: 0.3202 time to fit residues: 146.9331 Evaluate side-chains 313 residues out of total 1810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 285 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 159 ASN Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 196 MET Chi-restraints excluded: chain K residue 215 SER Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain E residue 2 ARG Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 422 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 178 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 70 optimal weight: 0.0980 chunk 172 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN ** A 256 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 = 0.3601 r_free = 0.3601 target = 0.093150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.071898 restraints weight = 31816.451| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.78 r_work: 0.3030 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17195 Z= 0.258 Angle : 0.603 9.696 23357 Z= 0.301 Chirality : 0.044 0.205 2560 Planarity : 0.004 0.076 3030 Dihedral : 8.851 170.217 2595 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.60 % Allowed : 15.64 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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 (0.19), residues: 2100 helix: 2.10 (0.18), residues: 899 sheet: -0.19 (0.27), residues: 381 loop : -0.66 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 57 HIS 0.014 0.001 HIS K 59 PHE 0.026 0.001 PHE K 225 TYR 0.014 0.001 TYR K 140 ARG 0.009 0.000 ARG K 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3830.13 seconds wall clock time: 70 minutes 46.22 seconds (4246.22 seconds total)