Starting phenix.real_space_refine on Thu Feb 15 17:14:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sn8_25214/02_2024/7sn8_25214_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sn8_25214/02_2024/7sn8_25214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sn8_25214/02_2024/7sn8_25214.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sn8_25214/02_2024/7sn8_25214.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sn8_25214/02_2024/7sn8_25214_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sn8_25214/02_2024/7sn8_25214_updated.pdb" } resolution = 2.74 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= 0.005 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 Zn 2 6.06 5 P 6 5.49 5 S 105 5.16 5 C 8214 2.51 5 N 2163 2.21 5 O 2370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 127": "OE1" <-> "OE2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 223": "OE1" <-> "OE2" Residue "D PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 300": "OD1" <-> "OD2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D GLU 308": "OE1" <-> "OE2" Residue "D PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 446": "OE1" <-> "OE2" Residue "D PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 515": "OD1" <-> "OD2" Residue "D TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 519": "OD1" <-> "OD2" Residue "K ASP 14": "OD1" <-> "OD2" Residue "K ARG 43": "NH1" <-> "NH2" Residue "K PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 105": "OE1" <-> "OE2" Residue "K ARG 108": "NH1" <-> "NH2" Residue "K PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 184": "OD1" <-> "OD2" Residue "K ASP 193": "OD1" <-> "OD2" Residue "K ARG 196": "NH1" <-> "NH2" Residue "K ASP 198": "OD1" <-> "OD2" Residue "K ARG 215": "NH1" <-> "NH2" Residue "K ARG 217": "NH1" <-> "NH2" Residue "K ARG 219": "NH1" <-> "NH2" Residue "K GLU 227": "OE1" <-> "OE2" Residue "K PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 244": "NH1" <-> "NH2" Residue "K ARG 258": "NH1" <-> "NH2" Residue "K TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 424": "NH1" <-> "NH2" Residue "K TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 464": "OE1" <-> "OE2" Residue "K ARG 508": "NH1" <-> "NH2" Residue "K ARG 512": "NH1" <-> "NH2" Residue "K ASP 520": "OD1" <-> "OD2" Residue "K ASP 521": "OD1" <-> "OD2" Residue "K ARG 527": "NH1" <-> "NH2" Residue "K GLU 530": "OE1" <-> "OE2" Residue "K ARG 531": "NH1" <-> "NH2" Residue "K GLU 538": "OE1" <-> "OE2" Residue "K GLU 549": "OE1" <-> "OE2" Residue "K ASP 565": "OD1" <-> "OD2" Residue "K GLU 566": "OE1" <-> "OE2" Residue "K ASP 568": "OD1" <-> "OD2" Residue "I ASP 9": "OD1" <-> "OD2" Residue "I ARG 23": "NH1" <-> "NH2" Residue "I GLU 32": "OE1" <-> "OE2" Residue "I PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 71": "OD1" <-> "OD2" Residue "I PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 93": "OD1" <-> "OD2" Residue "I GLU 139": "OE1" <-> "OE2" Residue "I GLU 170": "OE1" <-> "OE2" Residue "I PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 258": "OD1" <-> "OD2" Residue "I GLU 316": "OE1" <-> "OE2" Residue "I PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 344": "OE1" <-> "OE2" Residue "I TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 491": "OD1" <-> "OD2" Residue "I PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 581": "OE1" <-> "OE2" Residue "I ASP 588": "OD1" <-> "OD2" Residue "I ASP 597": "OD1" <-> "OD2" Residue "I ARG 606": "NH1" <-> "NH2" Residue "I GLU 618": "OE1" <-> "OE2" Residue "I ASP 619": "OD1" <-> "OD2" Residue "I ARG 640": "NH1" <-> "NH2" Residue "I ARG 644": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12860 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 3147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3147 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 4, 'TRANS': 394} Chain breaks: 5 Chain: "K" Number of atoms: 4665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4665 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 27, 'TRANS': 560} Chain breaks: 2 Chain: "I" Number of atoms: 5010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 5010 Classifications: {'peptide': 634} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 591} Chain breaks: 2 Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.94, per 1000 atoms: 0.54 Number of scatterers: 12860 At special positions: 0 Unit cell: (142.956, 122.379, 109.383, 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) Zn 2 29.99 S 105 16.00 P 6 15.00 O 2370 8.00 N 2163 7.00 C 8214 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 - 3.50 Amino acid : False - 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: 4.67 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 800 " pdb="ZN ZN K 800 " - pdb=" ND1 HIS K 70 " pdb="ZN ZN K 800 " - pdb=" NE2 HIS K 68 " pdb="ZN ZN K 800 " - pdb=" NE2 HIS K 157 " pdb=" ZN K 801 " pdb="ZN ZN K 801 " - pdb=" NE2 HIS K 73 " pdb="ZN ZN K 801 " - pdb=" NE2 HIS K 414 " 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3064 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 12 sheets defined 38.6% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain 'D' and resid 104 through 117 Processing helix chain 'D' and resid 128 through 141 Processing helix chain 'D' and resid 148 through 163 Processing helix chain 'D' and resid 170 through 183 Processing helix chain 'D' and resid 188 through 205 Processing helix chain 'D' and resid 211 through 227 removed outlier: 3.686A pdb=" N GLN D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ARG D 226 " --> pdb=" O LYS D 222 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 243 Processing helix chain 'D' and resid 253 through 262 removed outlier: 3.977A pdb=" N TYR D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE D 261 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP D 262 " --> pdb=" O ALA D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 281 Processing helix chain 'D' and resid 288 through 299 removed outlier: 3.717A pdb=" N LYS D 292 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL D 295 " --> pdb=" O LYS D 292 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU D 296 " --> pdb=" O ARG D 293 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS D 299 " --> pdb=" O GLU D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 4.093A pdb=" N GLU D 308 " --> pdb=" O CYS D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 349 removed outlier: 3.859A pdb=" N LEU D 348 " --> pdb=" O VAL D 344 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N CYS D 349 " --> pdb=" O CYS D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 364 removed outlier: 4.277A pdb=" N GLY D 364 " --> pdb=" O ALA D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 376 No H-bonds generated for 'chain 'D' and resid 374 through 376' Processing helix chain 'D' and resid 435 through 440 Processing helix chain 'D' and resid 446 through 461 removed outlier: 3.614A pdb=" N ALA D 450 " --> pdb=" O GLU D 446 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER D 461 " --> pdb=" O LYS D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 468 Processing helix chain 'D' and resid 470 through 478 removed outlier: 3.885A pdb=" N PHE D 477 " --> pdb=" O LEU D 473 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASN D 478 " --> pdb=" O VAL D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 495 Processing helix chain 'D' and resid 503 through 512 removed outlier: 3.707A pdb=" N ILE D 508 " --> pdb=" O ASP D 504 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER D 512 " --> pdb=" O ILE D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 530 Processing helix chain 'D' and resid 538 through 550 removed outlier: 3.593A pdb=" N VAL D 542 " --> pdb=" O CYS D 538 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP D 548 " --> pdb=" O GLN D 544 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL D 549 " --> pdb=" O LYS D 545 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU D 550 " --> pdb=" O LEU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 569 Processing helix chain 'K' and resid 42 through 44 No H-bonds generated for 'chain 'K' and resid 42 through 44' Processing helix chain 'K' and resid 71 through 74 No H-bonds generated for 'chain 'K' and resid 71 through 74' Processing helix chain 'K' and resid 77 through 82 Processing helix chain 'K' and resid 94 through 113 Proline residue: K 101 - end of helix removed outlier: 3.747A pdb=" N GLU K 113 " --> pdb=" O LYS K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 129 Processing helix chain 'K' and resid 214 through 231 removed outlier: 3.743A pdb=" N LYS K 231 " --> pdb=" O GLU K 227 " (cutoff:3.500A) Processing helix chain 'K' and resid 245 through 258 Processing helix chain 'K' and resid 275 through 281 removed outlier: 3.899A pdb=" N TYR K 279 " --> pdb=" O ALA K 275 " (cutoff:3.500A) Processing helix chain 'K' and resid 283 through 285 No H-bonds generated for 'chain 'K' and resid 283 through 285' Processing helix chain 'K' and resid 288 through 291 No H-bonds generated for 'chain 'K' and resid 288 through 291' Processing helix chain 'K' and resid 310 through 312 No H-bonds generated for 'chain 'K' and resid 310 through 312' Processing helix chain 'K' and resid 326 through 328 No H-bonds generated for 'chain 'K' and resid 326 through 328' Processing helix chain 'K' and resid 332 through 341 Processing helix chain 'K' and resid 359 through 364 Processing helix chain 'K' and resid 395 through 405 Processing helix chain 'K' and resid 417 through 431 Processing helix chain 'K' and resid 458 through 468 Processing helix chain 'K' and resid 497 through 504 Processing helix chain 'K' and resid 525 through 539 Processing helix chain 'K' and resid 580 through 595 removed outlier: 6.141A pdb=" N ASP K 584 " --> pdb=" O GLN K 581 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N TYR K 588 " --> pdb=" O ILE K 585 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ILE K 589 " --> pdb=" O GLY K 586 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 37 removed outlier: 3.653A pdb=" N LEU I 36 " --> pdb=" O GLN I 33 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN I 37 " --> pdb=" O THR I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 108 No H-bonds generated for 'chain 'I' and resid 106 through 108' Processing helix chain 'I' and resid 111 through 115 Processing helix chain 'I' and resid 128 through 147 Processing helix chain 'I' and resid 183 through 192 removed outlier: 3.843A pdb=" N LYS I 192 " --> pdb=" O GLY I 188 " (cutoff:3.500A) Processing helix chain 'I' and resid 273 through 289 Processing helix chain 'I' and resid 304 through 317 removed outlier: 3.950A pdb=" N GLU I 309 " --> pdb=" O TYR I 305 " (cutoff:3.500A) Processing helix chain 'I' and resid 332 through 341 removed outlier: 4.079A pdb=" N ASN I 340 " --> pdb=" O LEU I 336 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE I 341 " --> pdb=" O ALA I 337 " (cutoff:3.500A) Processing helix chain 'I' and resid 343 through 345 No H-bonds generated for 'chain 'I' and resid 343 through 345' Processing helix chain 'I' and resid 348 through 354 removed outlier: 4.320A pdb=" N LYS I 353 " --> pdb=" O ALA I 349 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL I 354 " --> pdb=" O LYS I 350 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 368 Processing helix chain 'I' and resid 383 through 386 No H-bonds generated for 'chain 'I' and resid 383 through 386' Processing helix chain 'I' and resid 404 through 411 removed outlier: 3.528A pdb=" N PHE I 408 " --> pdb=" O ASP I 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 429 through 432 No H-bonds generated for 'chain 'I' and resid 429 through 432' Processing helix chain 'I' and resid 434 through 436 No H-bonds generated for 'chain 'I' and resid 434 through 436' Processing helix chain 'I' and resid 454 through 464 removed outlier: 3.551A pdb=" N LYS I 459 " --> pdb=" O GLN I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 518 through 522 Processing helix chain 'I' and resid 575 through 577 No H-bonds generated for 'chain 'I' and resid 575 through 577' Processing helix chain 'I' and resid 590 through 594 Processing helix chain 'I' and resid 637 through 650 removed outlier: 3.841A pdb=" N LEU I 641 " --> pdb=" O PRO I 637 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS I 642 " --> pdb=" O THR I 638 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU I 643 " --> pdb=" O THR I 639 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N CYS I 650 " --> pdb=" O THR I 646 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'K' and resid 443 through 447 removed outlier: 5.471A pdb=" N CYS K 19 " --> pdb=" O LEU K 9 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N CYS K 63 " --> pdb=" O MET K 30 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 90 through 93 removed outlier: 3.835A pdb=" N MET K 92 " --> pdb=" O ILE K 134 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'K' and resid 142 through 144 removed outlier: 4.392A pdb=" N LEU K 148 " --> pdb=" O VAL K 144 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU K 199 " --> pdb=" O VAL K 174 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU K 434 " --> pdb=" O VAL K 410 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LEU K 412 " --> pdb=" O GLU K 434 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TYR K 436 " --> pdb=" O LEU K 412 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'K' and resid 383 through 386 removed outlier: 8.064A pdb=" N PHE K 322 " --> pdb=" O PRO K 264 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TYR K 266 " --> pdb=" O PHE K 322 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'K' and resid 369 through 371 Processing sheet with id= F, first strand: chain 'K' and resid 484 through 487 Processing sheet with id= G, first strand: chain 'K' and resid 512 through 520 Processing sheet with id= H, first strand: chain 'I' and resid 3 through 5 removed outlier: 6.585A pdb=" N VAL I 99 " --> pdb=" O MET I 25 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LYS I 123 " --> pdb=" O ILE I 100 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA I 126 " --> pdb=" O THR I 194 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 69 through 71 Processing sheet with id= J, first strand: chain 'I' and resid 202 through 204 removed outlier: 3.744A pdb=" N PHE I 208 " --> pdb=" O ILE I 204 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL I 259 " --> pdb=" O CYS I 234 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N VAL I 236 " --> pdb=" O VAL I 259 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE I 261 " --> pdb=" O VAL I 236 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL I 468 " --> pdb=" O LEU I 260 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N MET I 262 " --> pdb=" O VAL I 468 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL I 470 " --> pdb=" O MET I 262 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LYS I 493 " --> pdb=" O LEU I 469 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ILE I 471 " --> pdb=" O LYS I 493 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE I 495 " --> pdb=" O ILE I 471 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'I' and resid 294 through 296 removed outlier: 7.573A pdb=" N PHE I 394 " --> pdb=" O PRO I 324 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N PHE I 326 " --> pdb=" O PHE I 394 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'I' and resid 603 through 607 removed outlier: 4.407A pdb=" N THR I 620 " --> pdb=" O LEU I 615 " (cutoff:3.500A) 451 hydrogen bonds defined for protein. 1251 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: 3.72 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: 1.19 - 1.32: 2117 1.32 - 1.44: 3245 1.44 - 1.56: 7575 1.56 - 1.69: 6 1.69 - 1.81: 167 Bond restraints: 13110 Sorted by residual: bond pdb=" C5 IHP I 701 " pdb=" O15 IHP I 701 " ideal model delta sigma weight residual 1.389 1.465 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C1 IHP I 701 " pdb=" O11 IHP I 701 " ideal model delta sigma weight residual 1.392 1.463 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C3 IHP I 701 " pdb=" O13 IHP I 701 " ideal model delta sigma weight residual 1.393 1.463 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C6 IHP I 701 " pdb=" O16 IHP I 701 " ideal model delta sigma weight residual 1.394 1.463 -0.069 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C4 IHP I 701 " pdb=" O14 IHP I 701 " ideal model delta sigma weight residual 1.394 1.463 -0.069 2.00e-02 2.50e+03 1.19e+01 ... (remaining 13105 not shown) Histogram of bond angle deviations from ideal: 96.57 - 104.07: 227 104.07 - 111.58: 5803 111.58 - 119.09: 4945 119.09 - 126.60: 6574 126.60 - 134.10: 169 Bond angle restraints: 17718 Sorted by residual: angle pdb=" CA PHE D 444 " pdb=" C PHE D 444 " pdb=" O PHE D 444 " ideal model delta sigma weight residual 119.48 109.95 9.53 1.18e+00 7.18e-01 6.52e+01 angle pdb=" N PHE D 444 " pdb=" CA PHE D 444 " pdb=" C PHE D 444 " ideal model delta sigma weight residual 112.94 120.75 -7.81 1.41e+00 5.03e-01 3.07e+01 angle pdb=" C VAL I 544 " pdb=" N LYS I 545 " pdb=" CA LYS I 545 " ideal model delta sigma weight residual 121.54 131.29 -9.75 1.91e+00 2.74e-01 2.61e+01 angle pdb=" CA PRO I 428 " pdb=" C PRO I 428 " pdb=" O PRO I 428 " ideal model delta sigma weight residual 121.32 116.03 5.29 1.09e+00 8.42e-01 2.36e+01 angle pdb=" CA PHE D 444 " pdb=" C PHE D 444 " pdb=" N LEU D 445 " ideal model delta sigma weight residual 118.27 124.44 -6.17 1.30e+00 5.92e-01 2.25e+01 ... (remaining 17713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 7202 18.04 - 36.07: 685 36.07 - 54.11: 108 54.11 - 72.14: 25 72.14 - 90.18: 8 Dihedral angle restraints: 8028 sinusoidal: 3300 harmonic: 4728 Sorted by residual: dihedral pdb=" CA LYS I 545 " pdb=" C LYS I 545 " pdb=" N ASP I 546 " pdb=" CA ASP I 546 " ideal model delta harmonic sigma weight residual 180.00 150.89 29.11 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA ILE I 495 " pdb=" C ILE I 495 " pdb=" N THR I 496 " pdb=" CA THR I 496 " ideal model delta harmonic sigma weight residual 180.00 -152.06 -27.94 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA TYR I 355 " pdb=" C TYR I 355 " pdb=" N LEU I 356 " pdb=" CA LEU I 356 " ideal model delta harmonic sigma weight residual 180.00 152.37 27.63 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 8025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 1934 0.123 - 0.246: 81 0.246 - 0.370: 3 0.370 - 0.493: 1 0.493 - 0.616: 1 Chirality restraints: 2020 Sorted by residual: chirality pdb=" CA PHE D 444 " pdb=" N PHE D 444 " pdb=" C PHE D 444 " pdb=" CB PHE D 444 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.49e+00 chirality pdb=" CB VAL I 213 " pdb=" CA VAL I 213 " pdb=" CG1 VAL I 213 " pdb=" CG2 VAL I 213 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" C1 IHP I 701 " pdb=" C2 IHP I 701 " pdb=" C6 IHP I 701 " pdb=" O11 IHP I 701 " both_signs ideal model delta sigma weight residual False 2.32 2.65 -0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 2017 not shown) Planarity restraints: 2235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE I 394 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.74e+00 pdb=" C PHE I 394 " -0.051 2.00e-02 2.50e+03 pdb=" O PHE I 394 " 0.019 2.00e-02 2.50e+03 pdb=" N CYS I 395 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR I 81 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO I 82 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO I 82 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO I 82 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO I 428 " -0.011 2.00e-02 2.50e+03 2.36e-02 5.57e+00 pdb=" C PRO I 428 " 0.041 2.00e-02 2.50e+03 pdb=" O PRO I 428 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR I 429 " -0.014 2.00e-02 2.50e+03 ... (remaining 2232 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1162 2.74 - 3.28: 12357 3.28 - 3.82: 20741 3.82 - 4.36: 25382 4.36 - 4.90: 43218 Nonbonded interactions: 102860 Sorted by model distance: nonbonded pdb=" O ASP K 521 " pdb=" CA LYS K 570 " model vdw 2.204 3.470 nonbonded pdb=" O THR I 263 " pdb=" OH TYR I 475 " model vdw 2.240 2.440 nonbonded pdb=" O ALA K 268 " pdb=" OG1 THR K 324 " model vdw 2.255 2.440 nonbonded pdb=" O SER I 215 " pdb=" OG SER I 221 " model vdw 2.266 2.440 nonbonded pdb=" O ILE I 114 " pdb=" OG1 THR I 118 " model vdw 2.270 2.440 ... (remaining 102855 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.340 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 37.290 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 13110 Z= 0.403 Angle : 0.911 9.751 17718 Z= 0.506 Chirality : 0.059 0.616 2020 Planarity : 0.006 0.068 2235 Dihedral : 14.483 90.175 4964 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 0.28 % Allowed : 0.35 % Favored : 99.37 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.20), residues: 1597 helix: -0.38 (0.20), residues: 644 sheet: 0.18 (0.40), residues: 183 loop : -1.93 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 165 HIS 0.012 0.002 HIS K 414 PHE 0.033 0.002 PHE I 181 TYR 0.019 0.002 TYR I 4 ARG 0.008 0.001 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 164 time to evaluate : 1.475 Fit side-chains REVERT: D 105 ARG cc_start: 0.7836 (ttm-80) cc_final: 0.7619 (ttm170) REVERT: D 195 MET cc_start: 0.9098 (mmp) cc_final: 0.8628 (mmp) REVERT: D 207 HIS cc_start: 0.7189 (p-80) cc_final: 0.6753 (p-80) REVERT: D 443 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8492 (tt0) REVERT: D 565 ARG cc_start: 0.4649 (ttm-80) cc_final: 0.4068 (tpp-160) REVERT: D 566 LYS cc_start: 0.7263 (mtmt) cc_final: 0.6970 (mtmm) REVERT: K 511 MET cc_start: 0.6463 (ptp) cc_final: 0.5728 (ptp) REVERT: I 9 ASP cc_start: 0.7914 (t70) cc_final: 0.7662 (t70) REVERT: I 279 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6846 (mm-30) outliers start: 4 outliers final: 0 residues processed: 166 average time/residue: 1.4542 time to fit residues: 260.3489 Evaluate side-chains 133 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 443 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 76 optimal weight: 0.0970 chunk 93 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 329 HIS K 356 GLN I 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13110 Z= 0.182 Angle : 0.596 9.459 17718 Z= 0.314 Chirality : 0.045 0.166 2020 Planarity : 0.004 0.049 2235 Dihedral : 6.463 55.286 1779 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.40 % Allowed : 8.42 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.21), residues: 1597 helix: 0.27 (0.20), residues: 650 sheet: 0.47 (0.40), residues: 181 loop : -1.76 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 165 HIS 0.006 0.001 HIS I 245 PHE 0.013 0.001 PHE K 513 TYR 0.012 0.001 TYR K 386 ARG 0.006 0.000 ARG D 502 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 145 time to evaluate : 1.593 Fit side-chains REVERT: D 105 ARG cc_start: 0.7797 (ttm-80) cc_final: 0.7571 (ttm170) REVERT: D 195 MET cc_start: 0.9066 (mmp) cc_final: 0.8758 (mmt) REVERT: D 207 HIS cc_start: 0.7185 (p-80) cc_final: 0.6753 (p-80) REVERT: D 565 ARG cc_start: 0.4879 (ttm-80) cc_final: 0.4486 (tpp-160) REVERT: K 107 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.7405 (ttp) REVERT: K 125 MET cc_start: 0.8481 (ptp) cc_final: 0.8064 (ptm) REVERT: K 547 MET cc_start: 0.3241 (tpp) cc_final: 0.2549 (mpm) REVERT: I 155 ARG cc_start: 0.7538 (ptp-110) cc_final: 0.7202 (pmm-80) REVERT: I 279 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6855 (mm-30) REVERT: I 284 VAL cc_start: 0.8619 (p) cc_final: 0.8388 (t) REVERT: I 411 MET cc_start: 0.7570 (ttp) cc_final: 0.7352 (ttp) outliers start: 20 outliers final: 5 residues processed: 155 average time/residue: 1.3970 time to fit residues: 234.5157 Evaluate side-chains 134 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 292 LYS Chi-restraints excluded: chain K residue 107 MET Chi-restraints excluded: chain K residue 363 ILE Chi-restraints excluded: chain K residue 510 VAL Chi-restraints excluded: chain I residue 282 MET Chi-restraints excluded: chain I residue 534 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 40 optimal weight: 0.0270 chunk 145 optimal weight: 9.9990 chunk 157 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 overall best weight: 0.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 496 ASN ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13110 Z= 0.181 Angle : 0.566 7.963 17718 Z= 0.298 Chirality : 0.044 0.152 2020 Planarity : 0.004 0.046 2235 Dihedral : 5.902 51.493 1776 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 2.24 % Allowed : 10.94 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.61 (0.21), residues: 1597 helix: 0.62 (0.21), residues: 648 sheet: 0.62 (0.41), residues: 185 loop : -1.61 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 165 HIS 0.006 0.001 HIS K 414 PHE 0.013 0.001 PHE K 69 TYR 0.009 0.001 TYR D 260 ARG 0.003 0.000 ARG D 502 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 133 time to evaluate : 1.537 Fit side-chains revert: symmetry clash REVERT: D 105 ARG cc_start: 0.7814 (ttm-80) cc_final: 0.7577 (ttm170) REVERT: D 122 ASP cc_start: 0.7134 (OUTLIER) cc_final: 0.6494 (m-30) REVERT: D 195 MET cc_start: 0.9065 (mmp) cc_final: 0.8762 (mmt) REVERT: D 242 ARG cc_start: 0.7832 (ttm110) cc_final: 0.7533 (ttm110) REVERT: D 251 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.7101 (ppt170) REVERT: K 107 MET cc_start: 0.7634 (tmm) cc_final: 0.7412 (ttp) REVERT: K 347 MET cc_start: 0.8571 (ptt) cc_final: 0.8318 (ptp) REVERT: K 416 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.5885 (tm-30) REVERT: K 547 MET cc_start: 0.3442 (tpp) cc_final: 0.2324 (mtm) REVERT: I 88 MET cc_start: 0.8352 (mtt) cc_final: 0.8071 (mtt) REVERT: I 155 ARG cc_start: 0.7655 (ptp-110) cc_final: 0.7336 (pmm-80) REVERT: I 279 GLU cc_start: 0.7077 (mm-30) cc_final: 0.6834 (mm-30) outliers start: 32 outliers final: 12 residues processed: 153 average time/residue: 1.3851 time to fit residues: 229.5836 Evaluate side-chains 142 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 251 ARG Chi-restraints excluded: chain D residue 292 LYS Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain K residue 363 ILE Chi-restraints excluded: chain K residue 416 GLU Chi-restraints excluded: chain K residue 452 ILE Chi-restraints excluded: chain K residue 486 VAL Chi-restraints excluded: chain K residue 510 VAL Chi-restraints excluded: chain I residue 312 THR Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 533 VAL Chi-restraints excluded: chain I residue 534 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 0.0000 chunk 109 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 154 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 496 ASN ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13110 Z= 0.268 Angle : 0.617 11.093 17718 Z= 0.323 Chirality : 0.046 0.170 2020 Planarity : 0.004 0.051 2235 Dihedral : 6.015 54.750 1776 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 3.02 % Allowed : 12.13 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.59 (0.21), residues: 1597 helix: 0.66 (0.21), residues: 643 sheet: 0.54 (0.38), residues: 215 loop : -1.66 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 165 HIS 0.009 0.001 HIS K 414 PHE 0.020 0.002 PHE K 69 TYR 0.011 0.001 TYR D 302 ARG 0.004 0.000 ARG D 502 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 134 time to evaluate : 1.404 Fit side-chains REVERT: D 105 ARG cc_start: 0.7842 (ttm-80) cc_final: 0.7601 (ttm170) REVERT: D 122 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6503 (m-30) REVERT: D 169 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.7315 (pp30) REVERT: D 242 ARG cc_start: 0.7946 (ttm110) cc_final: 0.7720 (ttm170) REVERT: D 251 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7141 (ppt170) REVERT: D 513 LEU cc_start: 0.6792 (mt) cc_final: 0.6382 (mp) REVERT: K 50 TYR cc_start: 0.7629 (t80) cc_final: 0.7216 (t80) REVERT: K 125 MET cc_start: 0.8610 (ptp) cc_final: 0.8294 (ptm) REVERT: K 387 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7201 (mtt) REVERT: K 416 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6063 (tm-30) REVERT: K 547 MET cc_start: 0.3486 (tpp) cc_final: 0.2331 (mtm) REVERT: I 279 GLU cc_start: 0.7106 (mm-30) cc_final: 0.6862 (mm-30) outliers start: 43 outliers final: 22 residues processed: 160 average time/residue: 1.3503 time to fit residues: 234.6751 Evaluate side-chains 155 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 128 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 169 GLN Chi-restraints excluded: chain D residue 251 ARG Chi-restraints excluded: chain D residue 292 LYS Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 344 GLU Chi-restraints excluded: chain K residue 363 ILE Chi-restraints excluded: chain K residue 387 MET Chi-restraints excluded: chain K residue 416 GLU Chi-restraints excluded: chain K residue 452 ILE Chi-restraints excluded: chain K residue 486 VAL Chi-restraints excluded: chain K residue 510 VAL Chi-restraints excluded: chain I residue 196 MET Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 282 MET Chi-restraints excluded: chain I residue 312 THR Chi-restraints excluded: chain I residue 369 ASN Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 496 THR Chi-restraints excluded: chain I residue 520 LEU Chi-restraints excluded: chain I residue 533 VAL Chi-restraints excluded: chain I residue 534 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 0.8980 chunk 87 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 131 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 138 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 329 HIS K 496 ASN I 51 ASN I 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13110 Z= 0.171 Angle : 0.550 10.588 17718 Z= 0.288 Chirality : 0.043 0.146 2020 Planarity : 0.004 0.046 2235 Dihedral : 5.699 53.902 1776 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.52 % Allowed : 13.74 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.39 (0.21), residues: 1597 helix: 0.87 (0.21), residues: 644 sheet: 0.60 (0.39), residues: 197 loop : -1.54 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 165 HIS 0.006 0.001 HIS I 245 PHE 0.010 0.001 PHE K 69 TYR 0.009 0.001 TYR D 260 ARG 0.005 0.000 ARG D 502 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 138 time to evaluate : 1.543 Fit side-chains revert: symmetry clash REVERT: D 122 ASP cc_start: 0.7095 (OUTLIER) cc_final: 0.6487 (m-30) REVERT: D 251 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7248 (ppt170) REVERT: D 319 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.6492 (mtp180) REVERT: D 513 LEU cc_start: 0.6770 (mt) cc_final: 0.6407 (mp) REVERT: D 565 ARG cc_start: 0.5258 (tpp-160) cc_final: 0.4860 (mmm160) REVERT: K 50 TYR cc_start: 0.7673 (t80) cc_final: 0.7309 (t80) REVERT: K 125 MET cc_start: 0.8610 (ptp) cc_final: 0.8334 (ptm) REVERT: K 347 MET cc_start: 0.8570 (ptt) cc_final: 0.8295 (ptp) REVERT: K 416 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6085 (tm-30) REVERT: K 547 MET cc_start: 0.3470 (tpp) cc_final: 0.2627 (mpp) REVERT: I 9 ASP cc_start: 0.7731 (t70) cc_final: 0.7483 (t0) REVERT: I 88 MET cc_start: 0.8334 (mtt) cc_final: 0.8133 (mtt) REVERT: I 279 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6798 (mm-30) outliers start: 36 outliers final: 17 residues processed: 160 average time/residue: 1.4376 time to fit residues: 250.0633 Evaluate side-chains 151 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 251 ARG Chi-restraints excluded: chain D residue 292 LYS Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 319 ARG Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 107 MET Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 416 GLU Chi-restraints excluded: chain K residue 452 ILE Chi-restraints excluded: chain K residue 486 VAL Chi-restraints excluded: chain K residue 510 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 196 MET Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 520 LEU Chi-restraints excluded: chain I residue 533 VAL Chi-restraints excluded: chain I residue 541 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 38 optimal weight: 0.0070 chunk 154 optimal weight: 30.0000 chunk 128 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 496 ASN I 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13110 Z= 0.192 Angle : 0.561 8.830 17718 Z= 0.294 Chirality : 0.044 0.153 2020 Planarity : 0.004 0.046 2235 Dihedral : 5.657 55.515 1776 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 2.81 % Allowed : 15.01 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.32 (0.21), residues: 1597 helix: 0.92 (0.21), residues: 644 sheet: 0.65 (0.39), residues: 199 loop : -1.50 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 165 HIS 0.007 0.001 HIS K 329 PHE 0.015 0.001 PHE K 69 TYR 0.009 0.001 TYR D 260 ARG 0.005 0.000 ARG D 502 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 133 time to evaluate : 1.522 Fit side-chains REVERT: D 122 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6542 (m-30) REVERT: D 251 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7255 (ppt170) REVERT: D 319 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6495 (mtp180) REVERT: D 513 LEU cc_start: 0.6812 (mt) cc_final: 0.6444 (mp) REVERT: D 565 ARG cc_start: 0.5403 (tpp-160) cc_final: 0.4961 (mmm160) REVERT: K 50 TYR cc_start: 0.7780 (t80) cc_final: 0.7393 (t80) REVERT: K 107 MET cc_start: 0.7372 (tmm) cc_final: 0.7079 (ttp) REVERT: K 125 MET cc_start: 0.8621 (ptp) cc_final: 0.8344 (ptm) REVERT: K 347 MET cc_start: 0.8587 (ptt) cc_final: 0.8309 (ptp) REVERT: K 416 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6038 (tm-30) REVERT: K 547 MET cc_start: 0.3411 (tpp) cc_final: 0.2698 (mpt) REVERT: I 9 ASP cc_start: 0.7737 (t70) cc_final: 0.7494 (t0) REVERT: I 88 MET cc_start: 0.8374 (mtt) cc_final: 0.7833 (mtt) REVERT: I 279 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6854 (mm-30) REVERT: I 284 VAL cc_start: 0.8645 (OUTLIER) cc_final: 0.8338 (t) outliers start: 40 outliers final: 25 residues processed: 160 average time/residue: 1.4064 time to fit residues: 245.2943 Evaluate side-chains 156 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 251 ARG Chi-restraints excluded: chain D residue 292 LYS Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 319 ARG Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 416 GLU Chi-restraints excluded: chain K residue 452 ILE Chi-restraints excluded: chain K residue 486 VAL Chi-restraints excluded: chain K residue 510 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 196 MET Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 312 THR Chi-restraints excluded: chain I residue 369 ASN Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 520 LEU Chi-restraints excluded: chain I residue 533 VAL Chi-restraints excluded: chain I residue 534 THR Chi-restraints excluded: chain I residue 541 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 130 optimal weight: 0.7980 chunk 86 optimal weight: 8.9990 chunk 154 optimal weight: 20.0000 chunk 96 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 496 ASN K 507 ASN ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 13110 Z= 0.384 Angle : 0.688 8.648 17718 Z= 0.361 Chirality : 0.049 0.201 2020 Planarity : 0.005 0.054 2235 Dihedral : 6.188 57.540 1776 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 3.44 % Allowed : 15.64 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: -0.64 (0.21), residues: 1597 helix: 0.56 (0.21), residues: 644 sheet: 0.70 (0.38), residues: 211 loop : -1.68 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP I 157 HIS 0.013 0.002 HIS K 414 PHE 0.024 0.002 PHE K 69 TYR 0.013 0.002 TYR D 302 ARG 0.004 0.001 ARG D 502 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 126 time to evaluate : 1.562 Fit side-chains REVERT: D 105 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7690 (ttm170) REVERT: D 122 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6604 (m-30) REVERT: D 207 HIS cc_start: 0.7426 (p-80) cc_final: 0.6929 (p-80) REVERT: D 251 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7304 (ppt170) REVERT: D 513 LEU cc_start: 0.6803 (mt) cc_final: 0.6475 (mp) REVERT: D 565 ARG cc_start: 0.5379 (tpp-160) cc_final: 0.4889 (mmm160) REVERT: K 50 TYR cc_start: 0.7765 (t80) cc_final: 0.7377 (t80) REVERT: K 107 MET cc_start: 0.7485 (tmm) cc_final: 0.7218 (ttp) REVERT: K 125 MET cc_start: 0.8669 (ptp) cc_final: 0.8349 (ptm) REVERT: K 387 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.6870 (mtt) REVERT: K 416 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6143 (tm-30) REVERT: K 547 MET cc_start: 0.3512 (tpp) cc_final: 0.2189 (mtt) REVERT: I 9 ASP cc_start: 0.8047 (t70) cc_final: 0.7795 (t70) REVERT: I 279 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6921 (mm-30) REVERT: I 284 VAL cc_start: 0.8707 (OUTLIER) cc_final: 0.8329 (t) outliers start: 49 outliers final: 28 residues processed: 159 average time/residue: 1.2791 time to fit residues: 222.0076 Evaluate side-chains 160 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 126 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 251 ARG Chi-restraints excluded: chain D residue 292 LYS Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 363 ILE Chi-restraints excluded: chain K residue 387 MET Chi-restraints excluded: chain K residue 416 GLU Chi-restraints excluded: chain K residue 452 ILE Chi-restraints excluded: chain K residue 486 VAL Chi-restraints excluded: chain K residue 510 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 196 MET Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 282 MET Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 312 THR Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 369 ASN Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 496 THR Chi-restraints excluded: chain I residue 520 LEU Chi-restraints excluded: chain I residue 533 VAL Chi-restraints excluded: chain I residue 534 THR Chi-restraints excluded: chain I residue 541 VAL Chi-restraints excluded: chain I residue 621 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 496 ASN K 507 ASN I 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13110 Z= 0.284 Angle : 0.628 9.178 17718 Z= 0.330 Chirality : 0.047 0.175 2020 Planarity : 0.004 0.052 2235 Dihedral : 6.078 57.236 1776 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 3.09 % Allowed : 16.41 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: -0.63 (0.21), residues: 1597 helix: 0.57 (0.21), residues: 647 sheet: 0.65 (0.38), residues: 213 loop : -1.68 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 165 HIS 0.010 0.001 HIS K 414 PHE 0.019 0.002 PHE K 69 TYR 0.012 0.001 TYR D 302 ARG 0.004 0.000 ARG D 502 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 127 time to evaluate : 1.455 Fit side-chains revert: symmetry clash REVERT: D 105 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7713 (ttm170) REVERT: D 207 HIS cc_start: 0.7274 (p-80) cc_final: 0.6733 (p-80) REVERT: D 251 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7231 (ppt170) REVERT: D 513 LEU cc_start: 0.6783 (mt) cc_final: 0.6468 (mp) REVERT: D 565 ARG cc_start: 0.5409 (tpp-160) cc_final: 0.4858 (mmm160) REVERT: K 50 TYR cc_start: 0.7754 (t80) cc_final: 0.7328 (t80) REVERT: K 125 MET cc_start: 0.8648 (ptp) cc_final: 0.8342 (ptm) REVERT: K 305 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8335 (mm) REVERT: K 416 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6094 (tm-30) REVERT: K 547 MET cc_start: 0.3375 (tpp) cc_final: 0.2159 (mtt) REVERT: I 9 ASP cc_start: 0.8028 (t70) cc_final: 0.7812 (t70) REVERT: I 96 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7539 (mm-30) REVERT: I 279 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6911 (mm-30) REVERT: I 284 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8340 (t) outliers start: 44 outliers final: 29 residues processed: 157 average time/residue: 1.2330 time to fit residues: 213.1367 Evaluate side-chains 160 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 125 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 169 GLN Chi-restraints excluded: chain D residue 251 ARG Chi-restraints excluded: chain D residue 292 LYS Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 305 ILE Chi-restraints excluded: chain K residue 363 ILE Chi-restraints excluded: chain K residue 416 GLU Chi-restraints excluded: chain K residue 452 ILE Chi-restraints excluded: chain K residue 486 VAL Chi-restraints excluded: chain K residue 510 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 196 MET Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 312 THR Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 369 ASN Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 496 THR Chi-restraints excluded: chain I residue 520 LEU Chi-restraints excluded: chain I residue 533 VAL Chi-restraints excluded: chain I residue 534 THR Chi-restraints excluded: chain I residue 541 VAL Chi-restraints excluded: chain I residue 594 LEU Chi-restraints excluded: chain I residue 621 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 134 optimal weight: 0.5980 chunk 143 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 62 optimal weight: 0.5980 chunk 112 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 129 optimal weight: 0.1980 chunk 135 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 496 ASN K 507 ASN K 571 GLN I 51 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13110 Z= 0.167 Angle : 0.557 8.973 17718 Z= 0.293 Chirality : 0.043 0.151 2020 Planarity : 0.004 0.047 2235 Dihedral : 5.734 58.720 1776 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.95 % Allowed : 16.83 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: -0.37 (0.21), residues: 1597 helix: 0.87 (0.21), residues: 643 sheet: 0.62 (0.38), residues: 210 loop : -1.54 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 165 HIS 0.007 0.001 HIS K 329 PHE 0.012 0.001 PHE I 444 TYR 0.009 0.001 TYR D 302 ARG 0.005 0.000 ARG D 502 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 125 time to evaluate : 1.510 Fit side-chains revert: symmetry clash REVERT: D 251 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7271 (ppt170) REVERT: D 513 LEU cc_start: 0.6747 (mt) cc_final: 0.6439 (mp) REVERT: K 50 TYR cc_start: 0.7767 (t80) cc_final: 0.7333 (t80) REVERT: K 107 MET cc_start: 0.7329 (tmm) cc_final: 0.7078 (ttp) REVERT: K 125 MET cc_start: 0.8601 (ptp) cc_final: 0.8334 (ptm) REVERT: K 303 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8217 (pttt) REVERT: K 347 MET cc_start: 0.8595 (ptt) cc_final: 0.8123 (ttp) REVERT: K 547 MET cc_start: 0.3311 (tpp) cc_final: 0.2178 (mtt) REVERT: I 88 MET cc_start: 0.8379 (mtt) cc_final: 0.7988 (mtt) REVERT: I 96 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7482 (mm-30) REVERT: I 279 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6877 (mm-30) REVERT: I 284 VAL cc_start: 0.8672 (OUTLIER) cc_final: 0.8327 (t) outliers start: 42 outliers final: 27 residues processed: 156 average time/residue: 1.2128 time to fit residues: 207.1803 Evaluate side-chains 156 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 125 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 251 ARG Chi-restraints excluded: chain D residue 292 LYS Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 303 LYS Chi-restraints excluded: chain K residue 452 ILE Chi-restraints excluded: chain K residue 486 VAL Chi-restraints excluded: chain K residue 487 MET Chi-restraints excluded: chain K residue 510 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 196 MET Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 312 THR Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 369 ASN Chi-restraints excluded: chain I residue 421 ILE Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 520 LEU Chi-restraints excluded: chain I residue 533 VAL Chi-restraints excluded: chain I residue 534 THR Chi-restraints excluded: chain I residue 541 VAL Chi-restraints excluded: chain I residue 594 LEU Chi-restraints excluded: chain I residue 621 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 chunk 72 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 159 optimal weight: 7.9990 chunk 146 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 100 optimal weight: 0.5980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 496 ASN I 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13110 Z= 0.273 Angle : 0.618 8.279 17718 Z= 0.324 Chirality : 0.046 0.171 2020 Planarity : 0.004 0.050 2235 Dihedral : 5.899 55.933 1776 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 2.88 % Allowed : 17.11 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: -0.47 (0.21), residues: 1597 helix: 0.73 (0.21), residues: 647 sheet: 0.66 (0.38), residues: 213 loop : -1.59 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 165 HIS 0.009 0.001 HIS K 414 PHE 0.018 0.002 PHE K 69 TYR 0.021 0.001 TYR K 386 ARG 0.009 0.000 ARG D 502 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 127 time to evaluate : 1.484 Fit side-chains revert: symmetry clash REVERT: D 251 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7308 (ppt170) REVERT: D 513 LEU cc_start: 0.6755 (mt) cc_final: 0.6454 (mp) REVERT: D 565 ARG cc_start: 0.7145 (ptm160) cc_final: 0.5790 (mmm160) REVERT: K 50 TYR cc_start: 0.7818 (t80) cc_final: 0.7482 (t80) REVERT: K 107 MET cc_start: 0.7332 (tmm) cc_final: 0.7090 (ttp) REVERT: K 125 MET cc_start: 0.8653 (ptp) cc_final: 0.8348 (ptm) REVERT: K 347 MET cc_start: 0.8632 (ptt) cc_final: 0.8072 (ttp) REVERT: K 547 MET cc_start: 0.3460 (tpp) cc_final: 0.2223 (mtt) REVERT: I 96 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7488 (mm-30) REVERT: I 279 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6887 (mm-30) REVERT: I 284 VAL cc_start: 0.8696 (OUTLIER) cc_final: 0.8328 (t) outliers start: 41 outliers final: 32 residues processed: 155 average time/residue: 1.2128 time to fit residues: 205.7845 Evaluate side-chains 157 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 122 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 251 ARG Chi-restraints excluded: chain D residue 292 LYS Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 363 ILE Chi-restraints excluded: chain K residue 452 ILE Chi-restraints excluded: chain K residue 486 VAL Chi-restraints excluded: chain K residue 487 MET Chi-restraints excluded: chain K residue 510 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 196 MET Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 312 THR Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 369 ASN Chi-restraints excluded: chain I residue 411 MET Chi-restraints excluded: chain I residue 421 ILE Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 520 LEU Chi-restraints excluded: chain I residue 533 VAL Chi-restraints excluded: chain I residue 534 THR Chi-restraints excluded: chain I residue 541 VAL Chi-restraints excluded: chain I residue 594 LEU Chi-restraints excluded: chain I residue 621 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.2980 chunk 38 optimal weight: 9.9990 chunk 117 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 127 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 496 ASN I 51 ASN I 549 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.174240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.126058 restraints weight = 15414.319| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.04 r_work: 0.3404 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13110 Z= 0.155 Angle : 0.543 9.255 17718 Z= 0.285 Chirality : 0.043 0.143 2020 Planarity : 0.004 0.046 2235 Dihedral : 5.545 57.487 1776 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 1.89 % Allowed : 18.16 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: -0.23 (0.22), residues: 1597 helix: 1.00 (0.21), residues: 642 sheet: 0.74 (0.38), residues: 217 loop : -1.52 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 165 HIS 0.007 0.001 HIS K 329 PHE 0.011 0.001 PHE I 444 TYR 0.010 0.001 TYR I 4 ARG 0.009 0.000 ARG D 502 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4756.77 seconds wall clock time: 85 minutes 32.82 seconds (5132.82 seconds total)