Starting phenix.real_space_refine on Thu Apr 11 01:57:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjf_25924/04_2024/7tjf_25924_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjf_25924/04_2024/7tjf_25924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjf_25924/04_2024/7tjf_25924.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjf_25924/04_2024/7tjf_25924.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjf_25924/04_2024/7tjf_25924_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjf_25924/04_2024/7tjf_25924_updated.pdb" } resolution = 2.6 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 90 5.49 5 Mg 3 5.21 5 S 80 5.16 5 C 13126 2.51 5 N 3485 2.21 5 O 4341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 841": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 469": "OD1" <-> "OD2" Residue "C TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 329": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 21125 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3897 Classifications: {'peptide': 486} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 476} Chain breaks: 4 Chain: "B" Number of atoms: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2103 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 11, 'TRANS': 242} Chain breaks: 1 Chain: "C" Number of atoms: 4575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4575 Classifications: {'peptide': 554} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 537} Chain breaks: 5 Chain: "D" Number of atoms: 3536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3536 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 420} Chain breaks: 3 Chain: "E" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3608 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 21, 'TRANS': 418} Chain breaks: 3 Chain: "F" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1335 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 3, 'TRANS': 156} Chain: "G" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 832 Classifications: {'DNA': 41} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 40} Chain: "H" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 846 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "H" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Time building chain proxies: 11.54, per 1000 atoms: 0.55 Number of scatterers: 21125 At special positions: 0 Unit cell: (114.38, 127.28, 184.9, 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 80 16.00 P 90 15.00 Mg 3 11.99 O 4341 8.00 N 3485 7.00 C 13126 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: 8.96 Conformation dependent library (CDL) restraints added in 3.8 seconds 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4520 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 121 helices and 10 sheets defined 53.1% alpha, 7.3% beta 41 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 9.58 Creating SS restraints... Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 408 through 410 No H-bonds generated for 'chain 'A' and resid 408 through 410' Processing helix chain 'A' and resid 422 through 430 removed outlier: 4.278A pdb=" N VAL A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 468 Processing helix chain 'A' and resid 485 through 501 Processing helix chain 'A' and resid 521 through 533 removed outlier: 3.553A pdb=" N CYS A 524 " --> pdb=" O PRO A 521 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU A 528 " --> pdb=" O TYR A 525 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TRP A 529 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER A 533 " --> pdb=" O ASN A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 552 Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 577 through 587 removed outlier: 3.857A pdb=" N THR A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 608 Processing helix chain 'A' and resid 611 through 617 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 686 through 699 Processing helix chain 'A' and resid 703 through 725 Processing helix chain 'A' and resid 775 through 786 removed outlier: 3.814A pdb=" N THR A 785 " --> pdb=" O ALA A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 796 removed outlier: 3.580A pdb=" N ARG A 796 " --> pdb=" O THR A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 814 Processing helix chain 'A' and resid 822 through 835 Processing helix chain 'A' and resid 840 through 851 removed outlier: 4.943A pdb=" N LYS A 847 " --> pdb=" O MET A 843 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N THR A 848 " --> pdb=" O GLU A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 875 Processing helix chain 'A' and resid 898 through 907 Processing helix chain 'B' and resid 242 through 249 Processing helix chain 'B' and resid 263 through 265 No H-bonds generated for 'chain 'B' and resid 263 through 265' Processing helix chain 'B' and resid 271 through 284 removed outlier: 3.634A pdb=" N GLU B 283 " --> pdb=" O ASN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 309 removed outlier: 4.254A pdb=" N LYS B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N MET B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE B 301 " --> pdb=" O GLN B 297 " (cutoff:3.500A) Proline residue: B 302 - end of helix Processing helix chain 'B' and resid 323 through 330 Processing helix chain 'B' and resid 334 through 341 Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 399 through 413 removed outlier: 4.864A pdb=" N ASN B 413 " --> pdb=" O ASP B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 446 Processing helix chain 'B' and resid 461 through 464 Processing helix chain 'B' and resid 467 through 473 Processing helix chain 'B' and resid 489 through 492 removed outlier: 3.877A pdb=" N PHE B 492 " --> pdb=" O GLU B 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 489 through 492' Processing helix chain 'C' and resid 17 through 19 No H-bonds generated for 'chain 'C' and resid 17 through 19' Processing helix chain 'C' and resid 51 through 91 removed outlier: 3.882A pdb=" N GLN C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 156 Processing helix chain 'C' and resid 186 through 189 No H-bonds generated for 'chain 'C' and resid 186 through 189' Processing helix chain 'C' and resid 191 through 194 No H-bonds generated for 'chain 'C' and resid 191 through 194' Processing helix chain 'C' and resid 213 through 228 removed outlier: 3.913A pdb=" N SER C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LYS C 228 " --> pdb=" O LYS C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 248 Processing helix chain 'C' and resid 253 through 259 Processing helix chain 'C' and resid 272 through 287 removed outlier: 4.160A pdb=" N LYS C 275 " --> pdb=" O LYS C 272 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N TYR C 276 " --> pdb=" O GLY C 273 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY C 277 " --> pdb=" O PHE C 274 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASN C 278 " --> pdb=" O LYS C 275 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN C 279 " --> pdb=" O TYR C 276 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE C 281 " --> pdb=" O ASN C 278 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN C 282 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 307 Processing helix chain 'C' and resid 314 through 331 Processing helix chain 'C' and resid 333 through 338 removed outlier: 4.001A pdb=" N VAL C 336 " --> pdb=" O ALA C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 342 No H-bonds generated for 'chain 'C' and resid 340 through 342' Processing helix chain 'C' and resid 348 through 356 removed outlier: 4.068A pdb=" N ARG C 356 " --> pdb=" O LYS C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 370 Processing helix chain 'C' and resid 375 through 380 removed outlier: 3.518A pdb=" N SER C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU C 380 " --> pdb=" O GLU C 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 375 through 380' Processing helix chain 'C' and resid 389 through 395 removed outlier: 3.653A pdb=" N VAL C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU C 394 " --> pdb=" O GLU C 390 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE C 395 " --> pdb=" O PHE C 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 389 through 395' Processing helix chain 'C' and resid 402 through 415 Processing helix chain 'C' and resid 424 through 433 Processing helix chain 'C' and resid 436 through 440 Processing helix chain 'C' and resid 474 through 479 Processing helix chain 'C' and resid 483 through 492 Processing helix chain 'C' and resid 511 through 516 Processing helix chain 'C' and resid 520 through 529 removed outlier: 3.516A pdb=" N LEU C 527 " --> pdb=" O GLN C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 547 removed outlier: 3.846A pdb=" N THR C 547 " --> pdb=" O ALA C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 558 removed outlier: 3.980A pdb=" N LEU C 554 " --> pdb=" O LYS C 550 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG C 558 " --> pdb=" O LEU C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 570 Processing helix chain 'C' and resid 575 through 594 Processing helix chain 'D' and resid 47 through 61 Processing helix chain 'D' and resid 66 through 68 No H-bonds generated for 'chain 'D' and resid 66 through 68' Processing helix chain 'D' and resid 73 through 90 removed outlier: 4.510A pdb=" N ASP D 77 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N CYS D 78 " --> pdb=" O TYR D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 121 removed outlier: 3.800A pdb=" N GLN D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 155 Processing helix chain 'D' and resid 177 through 187 Processing helix chain 'D' and resid 219 through 221 No H-bonds generated for 'chain 'D' and resid 219 through 221' Processing helix chain 'D' and resid 229 through 240 Processing helix chain 'D' and resid 256 through 259 No H-bonds generated for 'chain 'D' and resid 256 through 259' Processing helix chain 'D' and resid 262 through 267 Processing helix chain 'D' and resid 281 through 292 Processing helix chain 'D' and resid 302 through 314 Processing helix chain 'D' and resid 319 through 330 Processing helix chain 'D' and resid 334 through 346 removed outlier: 3.565A pdb=" N SER D 340 " --> pdb=" O THR D 336 " (cutoff:3.500A) Proline residue: D 343 - end of helix Processing helix chain 'D' and resid 351 through 360 Processing helix chain 'D' and resid 362 through 371 Processing helix chain 'D' and resid 376 through 382 removed outlier: 3.540A pdb=" N LEU D 380 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER D 382 " --> pdb=" O GLY D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 400 Processing helix chain 'D' and resid 408 through 424 Processing helix chain 'D' and resid 453 through 465 removed outlier: 4.164A pdb=" N ASN D 458 " --> pdb=" O LYS D 454 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL D 459 " --> pdb=" O ASP D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 488 Processing helix chain 'D' and resid 493 through 495 No H-bonds generated for 'chain 'D' and resid 493 through 495' Processing helix chain 'D' and resid 499 through 501 No H-bonds generated for 'chain 'D' and resid 499 through 501' Processing helix chain 'D' and resid 510 through 516 Processing helix chain 'D' and resid 524 through 527 Processing helix chain 'E' and resid 12 through 21 Processing helix chain 'E' and resid 26 through 28 No H-bonds generated for 'chain 'E' and resid 26 through 28' Processing helix chain 'E' and resid 43 through 53 Processing helix chain 'E' and resid 70 through 88 Processing helix chain 'E' and resid 99 through 101 No H-bonds generated for 'chain 'E' and resid 99 through 101' Processing helix chain 'E' and resid 105 through 119 removed outlier: 4.246A pdb=" N GLN E 118 " --> pdb=" O ASN E 114 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR E 119 " --> pdb=" O ILE E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 137 No H-bonds generated for 'chain 'E' and resid 135 through 137' Processing helix chain 'E' and resid 145 through 155 removed outlier: 3.541A pdb=" N TYR E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASN E 153 " --> pdb=" O TYR E 149 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLU E 154 " --> pdb=" O ILE E 150 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU E 155 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 182 removed outlier: 4.135A pdb=" N TYR E 179 " --> pdb=" O PHE E 175 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER E 180 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N THR E 181 " --> pdb=" O GLN E 177 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N HIS E 182 " --> pdb=" O ARG E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 210 removed outlier: 5.685A pdb=" N GLY E 207 " --> pdb=" O MET E 203 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLU E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 221 removed outlier: 3.662A pdb=" N ILE E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 251 removed outlier: 6.031A pdb=" N SER E 249 " --> pdb=" O GLN E 245 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N TYR E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 272 Proline residue: E 267 - end of helix removed outlier: 3.894A pdb=" N ARG E 272 " --> pdb=" O LYS E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 278 No H-bonds generated for 'chain 'E' and resid 275 through 278' Processing helix chain 'E' and resid 281 through 287 Processing helix chain 'E' and resid 289 through 292 Processing helix chain 'E' and resid 326 through 340 Processing helix chain 'E' and resid 346 through 349 No H-bonds generated for 'chain 'E' and resid 346 through 349' Processing helix chain 'E' and resid 373 through 375 No H-bonds generated for 'chain 'E' and resid 373 through 375' Processing helix chain 'E' and resid 383 through 393 Processing helix chain 'E' and resid 418 through 429 Processing helix chain 'E' and resid 456 through 465 Processing helix chain 'E' and resid 471 through 475 removed outlier: 4.027A pdb=" N SER E 475 " --> pdb=" O ASP E 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 290 Processing helix chain 'F' and resid 296 through 312 removed outlier: 3.623A pdb=" N ASN F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N SER F 311 " --> pdb=" O ASN F 307 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG F 312 " --> pdb=" O ILE F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 331 removed outlier: 3.507A pdb=" N ILE F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 338 Processing helix chain 'F' and resid 340 through 353 removed outlier: 4.362A pdb=" N VAL F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SER F 348 " --> pdb=" O HIS F 344 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER F 352 " --> pdb=" O SER F 348 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 373 removed outlier: 3.659A pdb=" N GLU F 371 " --> pdb=" O LYS F 367 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 385 Processing helix chain 'F' and resid 394 through 401 removed outlier: 4.228A pdb=" N PHE F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 429 Processing sheet with id= A, first strand: chain 'A' and resid 620 through 624 removed outlier: 6.355A pdb=" N ILE A 561 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE A 596 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL A 563 " --> pdb=" O ILE A 596 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL A 598 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU A 565 " --> pdb=" O VAL A 598 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 657 through 659 removed outlier: 3.637A pdb=" N SER A 646 " --> pdb=" O LEU A 682 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 879 through 881 Processing sheet with id= D, first strand: chain 'B' and resid 475 through 479 removed outlier: 6.232A pdb=" N SER B 313 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N HIS B 478 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU B 315 " --> pdb=" O HIS B 478 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU B 420 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL B 453 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU B 422 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N SER B 455 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 424 " --> pdb=" O SER B 455 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 263 through 267 removed outlier: 6.826A pdb=" N THR C 104 " --> pdb=" O HIS C 264 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N LEU C 266 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N PHE C 106 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU C 199 " --> pdb=" O LYS C 233 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N SER C 235 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N MET C 201 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE C 237 " --> pdb=" O MET C 201 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE C 203 " --> pdb=" O ILE C 237 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ASN C 239 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N PHE C 205 " --> pdb=" O ASN C 239 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 534 through 536 Processing sheet with id= G, first strand: chain 'D' and resid 271 through 274 removed outlier: 4.474A pdb=" N ARG D 271 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL D 212 " --> pdb=" O CYS D 246 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N PHE D 248 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE D 214 " --> pdb=" O PHE D 248 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N CYS D 250 " --> pdb=" O PHE D 214 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N PHE D 216 " --> pdb=" O CYS D 250 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 469 through 471 Processing sheet with id= I, first strand: chain 'E' and resid 185 through 189 removed outlier: 8.945A pdb=" N LEU E 33 " --> pdb=" O ILE E 164 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE E 166 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N LEU E 35 " --> pdb=" O PHE E 166 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TYR E 168 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N GLY E 37 " --> pdb=" O TYR E 168 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N MET E 170 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR E 126 " --> pdb=" O ASN E 163 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LYS E 165 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU E 128 " --> pdb=" O LYS E 165 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE E 167 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU E 130 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR E 169 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU E 132 " --> pdb=" O THR E 169 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 433 through 435 773 hydrogen bonds defined for protein. 2253 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 8.84 Time building geometry restraints manager: 9.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3241 1.31 - 1.44: 6093 1.44 - 1.57: 11768 1.57 - 1.70: 177 1.70 - 1.83: 132 Bond restraints: 21411 Sorted by residual: bond pdb=" C PRO C 27 " pdb=" O PRO C 27 " ideal model delta sigma weight residual 1.233 1.181 0.052 1.21e-02 6.83e+03 1.88e+01 bond pdb=" C LEU A 568 " pdb=" O LEU A 568 " ideal model delta sigma weight residual 1.236 1.184 0.052 1.28e-02 6.10e+03 1.64e+01 bond pdb=" C ASP A 569 " pdb=" O ASP A 569 " ideal model delta sigma weight residual 1.236 1.186 0.051 1.26e-02 6.30e+03 1.62e+01 bond pdb=" C ARG D 227 " pdb=" O ARG D 227 " ideal model delta sigma weight residual 1.235 1.188 0.047 1.26e-02 6.30e+03 1.38e+01 bond pdb=" C ARG D 227 " pdb=" N GLN D 228 " ideal model delta sigma weight residual 1.334 1.289 0.045 1.25e-02 6.40e+03 1.28e+01 ... (remaining 21406 not shown) Histogram of bond angle deviations from ideal: 95.24 - 104.18: 501 104.18 - 113.12: 11701 113.12 - 122.05: 13097 122.05 - 130.99: 3888 130.99 - 139.93: 111 Bond angle restraints: 29298 Sorted by residual: angle pdb=" CB MET A 779 " pdb=" CG MET A 779 " pdb=" SD MET A 779 " ideal model delta sigma weight residual 112.70 129.59 -16.89 3.00e+00 1.11e-01 3.17e+01 angle pdb=" C PRO C 27 " pdb=" CA PRO C 27 " pdb=" CB PRO C 27 " ideal model delta sigma weight residual 111.12 118.02 -6.90 1.29e+00 6.01e-01 2.86e+01 angle pdb=" C TYR C 26 " pdb=" CA TYR C 26 " pdb=" CB TYR C 26 " ideal model delta sigma weight residual 110.17 119.92 -9.75 1.97e+00 2.58e-01 2.45e+01 angle pdb=" CA GLU C 59 " pdb=" CB GLU C 59 " pdb=" CG GLU C 59 " ideal model delta sigma weight residual 114.10 123.80 -9.70 2.00e+00 2.50e-01 2.35e+01 angle pdb=" CA LEU A 461 " pdb=" CB LEU A 461 " pdb=" CG LEU A 461 " ideal model delta sigma weight residual 116.30 133.25 -16.95 3.50e+00 8.16e-02 2.34e+01 ... (remaining 29293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.16: 10625 18.16 - 36.32: 1452 36.32 - 54.48: 603 54.48 - 72.64: 113 72.64 - 90.80: 38 Dihedral angle restraints: 12831 sinusoidal: 5909 harmonic: 6922 Sorted by residual: dihedral pdb=" CA VAL E 8 " pdb=" C VAL E 8 " pdb=" N ALA E 9 " pdb=" CA ALA E 9 " ideal model delta harmonic sigma weight residual -180.00 -152.66 -27.34 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA LYS E 431 " pdb=" C LYS E 431 " pdb=" N LEU E 432 " pdb=" CA LEU E 432 " ideal model delta harmonic sigma weight residual 180.00 156.78 23.22 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA PHE B 475 " pdb=" C PHE B 475 " pdb=" N VAL B 476 " pdb=" CA VAL B 476 " ideal model delta harmonic sigma weight residual 180.00 157.02 22.98 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 12828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2655 0.060 - 0.121: 577 0.121 - 0.181: 75 0.181 - 0.242: 12 0.242 - 0.302: 3 Chirality restraints: 3322 Sorted by residual: chirality pdb=" CB THR A 474 " pdb=" CA THR A 474 " pdb=" OG1 THR A 474 " pdb=" CG2 THR A 474 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CB ILE E 326 " pdb=" CA ILE E 326 " pdb=" CG1 ILE E 326 " pdb=" CG2 ILE E 326 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB THR E 87 " pdb=" CA THR E 87 " pdb=" OG1 THR E 87 " pdb=" CG2 THR E 87 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 3319 not shown) Planarity restraints: 3392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 25 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C VAL C 25 " 0.056 2.00e-02 2.50e+03 pdb=" O VAL C 25 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR C 26 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 332 " 0.022 2.00e-02 2.50e+03 2.44e-02 1.04e+01 pdb=" CG PHE F 332 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE F 332 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE F 332 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE F 332 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE F 332 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 332 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 484 " 0.049 5.00e-02 4.00e+02 7.48e-02 8.95e+00 pdb=" N PRO B 485 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 485 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 485 " 0.041 5.00e-02 4.00e+02 ... (remaining 3389 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.42: 115 2.42 - 3.04: 10978 3.04 - 3.66: 34312 3.66 - 4.28: 53253 4.28 - 4.90: 82399 Nonbonded interactions: 181057 Sorted by model distance: nonbonded pdb=" OD1 ASP E 136 " pdb=" O HOH E1101 " model vdw 1.795 2.440 nonbonded pdb=" O PRO B 415 " pdb=" O HOH B 701 " model vdw 1.811 2.440 nonbonded pdb=" OD1 ASP A 867 " pdb=" O HOH A1101 " model vdw 1.879 2.440 nonbonded pdb=" O ILE E 184 " pdb=" O HOH E1102 " model vdw 1.948 2.440 nonbonded pdb=" OD2 ASP B 479 " pdb=" O HOH B 702 " model vdw 1.996 2.440 ... (remaining 181052 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: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.910 Check model and map are aligned: 0.320 Set scattering table: 0.180 Process input model: 65.550 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 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 0.073 21411 Z= 0.301 Angle : 0.868 16.948 29298 Z= 0.478 Chirality : 0.051 0.302 3322 Planarity : 0.006 0.084 3392 Dihedral : 19.812 90.804 8311 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.87 % Allowed : 17.86 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.15), residues: 2283 helix: -1.12 (0.12), residues: 1279 sheet: 0.14 (0.32), residues: 222 loop : -1.00 (0.19), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP F 317 HIS 0.026 0.002 HIS E 241 PHE 0.057 0.002 PHE F 332 TYR 0.025 0.002 TYR F 300 ARG 0.018 0.001 ARG F 393 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 352 time to evaluate : 2.512 Fit side-chains revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7559 (tp30) REVERT: C 395 PHE cc_start: 0.7118 (m-80) cc_final: 0.6621 (m-10) REVERT: C 454 HIS cc_start: 0.7624 (t70) cc_final: 0.7136 (t70) REVERT: E 212 ASP cc_start: 0.8344 (t70) cc_final: 0.8124 (t0) REVERT: E 284 LEU cc_start: 0.8997 (tp) cc_final: 0.8793 (tp) REVERT: F 277 TYR cc_start: 0.8325 (m-80) cc_final: 0.7815 (m-80) REVERT: F 287 ARG cc_start: 0.8218 (mtt-85) cc_final: 0.7962 (ttp-110) REVERT: F 344 HIS cc_start: 0.7439 (t-90) cc_final: 0.7055 (m-70) REVERT: F 363 ILE cc_start: 0.7964 (pt) cc_final: 0.7758 (pp) REVERT: F 364 GLU cc_start: 0.8158 (tt0) cc_final: 0.7851 (tm-30) REVERT: F 368 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8551 (mt) REVERT: F 400 ARG cc_start: 0.8221 (mtp180) cc_final: 0.8014 (mtm180) REVERT: F 414 THR cc_start: 0.8797 (p) cc_final: 0.8152 (p) outliers start: 40 outliers final: 13 residues processed: 384 average time/residue: 1.6562 time to fit residues: 706.7633 Evaluate side-chains 239 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 225 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 357 CYS Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 368 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 201 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 217 optimal weight: 9.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 405 GLN B 493 GLN C 253 GLN C 271 ASN C 312 HIS C 370 GLN C 532 ASN D 155 GLN ** D 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN E 241 HIS F 307 ASN F 318 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21411 Z= 0.278 Angle : 0.570 8.933 29298 Z= 0.307 Chirality : 0.042 0.145 3322 Planarity : 0.004 0.065 3392 Dihedral : 18.485 80.792 3574 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.61 % Allowed : 19.82 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.16), residues: 2283 helix: 0.24 (0.14), residues: 1272 sheet: 0.37 (0.32), residues: 212 loop : -0.59 (0.20), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 526 HIS 0.007 0.001 HIS E 241 PHE 0.017 0.001 PHE D 363 TYR 0.021 0.002 TYR C 528 ARG 0.010 0.001 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 224 time to evaluate : 2.579 Fit side-chains REVERT: A 420 GLU cc_start: 0.7783 (mm-30) cc_final: 0.6796 (tm-30) REVERT: A 425 LYS cc_start: 0.8911 (mmmt) cc_final: 0.8411 (mmmt) REVERT: B 390 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8162 (ttt90) REVERT: C 454 HIS cc_start: 0.7655 (t70) cc_final: 0.7100 (t70) REVERT: D 418 MET cc_start: 0.8546 (ttt) cc_final: 0.8328 (ttt) REVERT: D 493 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7157 (mp10) REVERT: E 212 ASP cc_start: 0.8394 (t70) cc_final: 0.8147 (t0) REVERT: E 437 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6760 (ppp) REVERT: E 441 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8012 (tp) REVERT: F 277 TYR cc_start: 0.8232 (m-80) cc_final: 0.7807 (m-80) REVERT: F 284 GLU cc_start: 0.8090 (tp30) cc_final: 0.7843 (tp30) REVERT: F 344 HIS cc_start: 0.7529 (t-90) cc_final: 0.7131 (m-70) REVERT: F 400 ARG cc_start: 0.8294 (mtp180) cc_final: 0.8053 (mtm180) outliers start: 56 outliers final: 20 residues processed: 265 average time/residue: 1.6680 time to fit residues: 493.9997 Evaluate side-chains 217 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 193 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain D residue 417 LYS Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 493 GLN Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 437 MET Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 278 CYS Chi-restraints excluded: chain F residue 362 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 120 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 217 optimal weight: 6.9990 chunk 234 optimal weight: 8.9990 chunk 193 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 ASN C 271 ASN C 313 ASN C 371 HIS D 96 HIS D 155 GLN ** D 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN F 307 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 21411 Z= 0.370 Angle : 0.584 7.907 29298 Z= 0.315 Chirality : 0.044 0.156 3322 Planarity : 0.004 0.060 3392 Dihedral : 18.592 74.784 3559 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.73 % Allowed : 18.61 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.17), residues: 2283 helix: 0.65 (0.14), residues: 1269 sheet: 0.26 (0.33), residues: 200 loop : -0.41 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 526 HIS 0.005 0.001 HIS C 62 PHE 0.023 0.002 PHE C 408 TYR 0.022 0.002 TYR C 483 ARG 0.007 0.000 ARG F 287 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 211 time to evaluate : 2.430 Fit side-chains revert: symmetry clash REVERT: A 576 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.7418 (pp30) REVERT: B 390 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8363 (ttt90) REVERT: C 454 HIS cc_start: 0.7651 (t70) cc_final: 0.7342 (t70) REVERT: D 186 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9218 (mp) REVERT: D 493 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7841 (mp10) REVERT: E 217 LYS cc_start: 0.7772 (mmpt) cc_final: 0.7152 (mttm) REVERT: E 245 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8233 (mp10) REVERT: E 437 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6764 (ppp) REVERT: E 441 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8034 (tp) REVERT: F 277 TYR cc_start: 0.8177 (m-80) cc_final: 0.7831 (m-80) REVERT: F 284 GLU cc_start: 0.7637 (tp30) cc_final: 0.6342 (tp30) REVERT: F 287 ARG cc_start: 0.8351 (ttp80) cc_final: 0.8122 (ttp-110) outliers start: 80 outliers final: 30 residues processed: 274 average time/residue: 1.5825 time to fit residues: 485.8207 Evaluate side-chains 226 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 189 time to evaluate : 3.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 417 LYS Chi-restraints excluded: chain D residue 453 LYS Chi-restraints excluded: chain D residue 454 LYS Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 493 GLN Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 437 MET Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 362 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 214 optimal weight: 8.9990 chunk 163 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 chunk 218 optimal weight: 7.9990 chunk 231 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 206 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 271 ASN D 155 GLN ** D 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN F 307 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 21411 Z= 0.389 Angle : 0.579 7.830 29298 Z= 0.313 Chirality : 0.044 0.164 3322 Planarity : 0.004 0.058 3392 Dihedral : 18.584 75.612 3558 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.40 % Allowed : 19.40 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.17), residues: 2283 helix: 0.84 (0.15), residues: 1277 sheet: 0.25 (0.33), residues: 200 loop : -0.33 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 526 HIS 0.006 0.001 HIS C 62 PHE 0.018 0.002 PHE D 363 TYR 0.021 0.002 TYR C 483 ARG 0.014 0.001 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 206 time to evaluate : 2.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 518 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8049 (mtm) REVERT: A 576 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.7418 (pp30) REVERT: A 859 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7645 (tt0) REVERT: B 390 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8399 (ttt90) REVERT: B 448 ARG cc_start: 0.9306 (OUTLIER) cc_final: 0.8740 (mmm160) REVERT: C 454 HIS cc_start: 0.7593 (t70) cc_final: 0.7262 (t70) REVERT: D 186 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9199 (mp) REVERT: D 270 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.7255 (mp10) REVERT: D 493 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7897 (mp10) REVERT: E 245 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8238 (mp10) REVERT: E 441 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8021 (tp) REVERT: F 277 TYR cc_start: 0.8227 (m-80) cc_final: 0.7863 (m-80) REVERT: F 364 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7352 (tm-30) REVERT: F 368 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8520 (mt) outliers start: 73 outliers final: 31 residues processed: 262 average time/residue: 1.6261 time to fit residues: 476.8491 Evaluate side-chains 236 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 193 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain D residue 417 LYS Chi-restraints excluded: chain D residue 453 LYS Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 491 GLN Chi-restraints excluded: chain D residue 493 GLN Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain F residue 368 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 192 optimal weight: 9.9990 chunk 131 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 197 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 GLN C 271 ASN C 313 ASN C 370 GLN D 155 GLN ** D 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN F 307 ASN F 318 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21411 Z= 0.191 Angle : 0.504 7.489 29298 Z= 0.275 Chirality : 0.040 0.157 3322 Planarity : 0.003 0.055 3392 Dihedral : 18.253 84.952 3558 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.52 % Allowed : 20.38 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.17), residues: 2283 helix: 1.19 (0.15), residues: 1270 sheet: 0.24 (0.33), residues: 200 loop : -0.21 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 494 HIS 0.005 0.001 HIS C 69 PHE 0.024 0.001 PHE C 408 TYR 0.018 0.001 TYR F 306 ARG 0.007 0.000 ARG F 287 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 205 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7459 (mm-30) REVERT: A 425 LYS cc_start: 0.8914 (mmmm) cc_final: 0.8666 (mmpt) REVERT: A 518 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.8068 (mtm) REVERT: A 653 LYS cc_start: 0.8629 (ptpt) cc_final: 0.8287 (mptt) REVERT: A 859 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7602 (tt0) REVERT: C 454 HIS cc_start: 0.7569 (t70) cc_final: 0.7246 (t70) REVERT: C 552 GLU cc_start: 0.8247 (mp0) cc_final: 0.8036 (mp0) REVERT: C 592 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7951 (tm-30) REVERT: D 54 ARG cc_start: 0.8138 (ttm110) cc_final: 0.7768 (ttm110) REVERT: D 186 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9208 (mp) REVERT: D 493 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7864 (mp10) REVERT: E 212 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8203 (t0) REVERT: E 217 LYS cc_start: 0.7800 (mmpt) cc_final: 0.7164 (mttm) REVERT: E 245 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8222 (mp10) REVERT: E 277 ASN cc_start: 0.7948 (m-40) cc_final: 0.7664 (m-40) REVERT: E 441 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.8023 (tp) REVERT: F 277 TYR cc_start: 0.8272 (m-80) cc_final: 0.7821 (m-80) outliers start: 54 outliers final: 25 residues processed: 240 average time/residue: 1.3688 time to fit residues: 366.5125 Evaluate side-chains 226 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 193 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 512 ASP Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 425 ARG Chi-restraints excluded: chain D residue 453 LYS Chi-restraints excluded: chain D residue 454 LYS Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 491 GLN Chi-restraints excluded: chain D residue 493 GLN Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 212 ASP Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 414 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 77 optimal weight: 7.9990 chunk 208 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 191 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 342 GLN C 271 ASN ** D 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN F 307 ASN F 318 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 21411 Z= 0.420 Angle : 0.591 7.774 29298 Z= 0.317 Chirality : 0.045 0.164 3322 Planarity : 0.004 0.056 3392 Dihedral : 18.564 78.528 3558 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.45 % Allowed : 19.96 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.17), residues: 2283 helix: 1.07 (0.15), residues: 1276 sheet: 0.31 (0.33), residues: 200 loop : -0.25 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 526 HIS 0.006 0.001 HIS C 62 PHE 0.031 0.002 PHE C 412 TYR 0.022 0.002 TYR C 483 ARG 0.015 0.001 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 194 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7416 (mm-30) REVERT: A 425 LYS cc_start: 0.8940 (mmmm) cc_final: 0.8642 (mmpt) REVERT: A 518 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.8022 (mtm) REVERT: A 576 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.7469 (pp30) REVERT: A 859 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7638 (tt0) REVERT: B 448 ARG cc_start: 0.9308 (OUTLIER) cc_final: 0.8755 (mmm160) REVERT: C 454 HIS cc_start: 0.7640 (t70) cc_final: 0.7348 (t70) REVERT: C 592 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7971 (tm-30) REVERT: D 54 ARG cc_start: 0.8175 (ttm110) cc_final: 0.7842 (ttm110) REVERT: D 186 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9211 (mp) REVERT: D 270 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.7185 (mp10) REVERT: D 493 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7975 (mp10) REVERT: E 203 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.8183 (ptp) REVERT: E 212 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8117 (t0) REVERT: E 217 LYS cc_start: 0.7786 (mmpt) cc_final: 0.7127 (mttm) REVERT: E 245 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8267 (mp10) REVERT: E 277 ASN cc_start: 0.8143 (m-40) cc_final: 0.7830 (m-40) REVERT: E 441 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8085 (tp) REVERT: F 277 TYR cc_start: 0.8261 (m-80) cc_final: 0.7780 (m-80) REVERT: F 312 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7931 (ptt180) outliers start: 74 outliers final: 34 residues processed: 251 average time/residue: 1.5551 time to fit residues: 438.5523 Evaluate side-chains 235 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 188 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain D residue 425 ARG Chi-restraints excluded: chain D residue 453 LYS Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 491 GLN Chi-restraints excluded: chain D residue 493 GLN Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 212 ASP Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 312 ARG Chi-restraints excluded: chain F residue 414 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 222 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 230 optimal weight: 8.9990 chunk 144 optimal weight: 0.4980 chunk 140 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 271 ASN C 313 ASN C 470 ASN ** D 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN E 82 GLN F 307 ASN F 318 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21411 Z= 0.187 Angle : 0.505 8.215 29298 Z= 0.276 Chirality : 0.040 0.182 3322 Planarity : 0.003 0.054 3392 Dihedral : 18.146 89.278 3558 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.61 % Allowed : 20.85 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.17), residues: 2283 helix: 1.34 (0.15), residues: 1278 sheet: 0.30 (0.33), residues: 200 loop : -0.19 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 494 HIS 0.005 0.001 HIS C 69 PHE 0.021 0.001 PHE C 408 TYR 0.018 0.001 TYR F 306 ARG 0.005 0.000 ARG C 442 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 196 time to evaluate : 2.539 Fit side-chains revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7468 (mm-30) REVERT: A 425 LYS cc_start: 0.8914 (mmmm) cc_final: 0.8644 (mmpt) REVERT: A 518 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.8042 (mtm) REVERT: A 653 LYS cc_start: 0.8661 (ptpt) cc_final: 0.8322 (mptt) REVERT: A 859 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7583 (tt0) REVERT: C 454 HIS cc_start: 0.7623 (t70) cc_final: 0.7305 (t70) REVERT: C 592 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7949 (tm-30) REVERT: D 54 ARG cc_start: 0.8144 (ttm110) cc_final: 0.7817 (ttm110) REVERT: D 186 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9202 (mp) REVERT: D 493 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7971 (mp10) REVERT: E 172 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7691 (mm-30) REVERT: E 212 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.8181 (t0) REVERT: E 217 LYS cc_start: 0.7738 (mmpt) cc_final: 0.7144 (mttm) REVERT: E 245 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8223 (mp10) REVERT: E 277 ASN cc_start: 0.7832 (m-40) cc_final: 0.7575 (m-40) REVERT: E 437 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.7013 (pmm) REVERT: E 441 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.7892 (tp) REVERT: F 277 TYR cc_start: 0.8246 (m-80) cc_final: 0.7656 (m-80) REVERT: F 312 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7955 (ptt180) outliers start: 56 outliers final: 30 residues processed: 235 average time/residue: 1.5994 time to fit residues: 420.5294 Evaluate side-chains 229 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 188 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 512 ASP Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain D residue 453 LYS Chi-restraints excluded: chain D residue 454 LYS Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 491 GLN Chi-restraints excluded: chain D residue 493 GLN Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 212 ASP Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 437 MET Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 312 ARG Chi-restraints excluded: chain F residue 414 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 142 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 181 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN E 82 GLN F 307 ASN F 318 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21411 Z= 0.240 Angle : 0.529 8.676 29298 Z= 0.286 Chirality : 0.041 0.163 3322 Planarity : 0.003 0.064 3392 Dihedral : 18.184 87.792 3557 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.38 % Allowed : 21.74 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.17), residues: 2283 helix: 1.38 (0.15), residues: 1278 sheet: 0.32 (0.33), residues: 200 loop : -0.17 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 494 HIS 0.004 0.001 HIS C 69 PHE 0.033 0.001 PHE C 412 TYR 0.019 0.001 TYR F 306 ARG 0.017 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 189 time to evaluate : 2.998 Fit side-chains REVERT: A 425 LYS cc_start: 0.8947 (mmmm) cc_final: 0.8700 (mmmt) REVERT: A 518 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.8037 (mtm) REVERT: A 653 LYS cc_start: 0.8693 (ptpt) cc_final: 0.8361 (mptt) REVERT: A 859 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7600 (tt0) REVERT: C 454 HIS cc_start: 0.7637 (t70) cc_final: 0.7320 (t70) REVERT: C 592 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7965 (tm-30) REVERT: D 54 ARG cc_start: 0.8164 (ttm110) cc_final: 0.7842 (ttm110) REVERT: D 186 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9207 (mp) REVERT: D 493 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8017 (mp10) REVERT: E 212 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.8165 (t0) REVERT: E 238 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8464 (t0) REVERT: E 245 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8247 (mp10) REVERT: E 277 ASN cc_start: 0.7792 (m-40) cc_final: 0.7521 (m-40) REVERT: E 437 MET cc_start: 0.7207 (OUTLIER) cc_final: 0.6778 (pmm) REVERT: E 441 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.7942 (tp) REVERT: F 277 TYR cc_start: 0.8269 (m-80) cc_final: 0.7654 (m-80) REVERT: F 312 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7966 (ptt180) outliers start: 51 outliers final: 32 residues processed: 228 average time/residue: 1.5748 time to fit residues: 403.2601 Evaluate side-chains 228 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 185 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 512 ASP Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain D residue 453 LYS Chi-restraints excluded: chain D residue 454 LYS Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 491 GLN Chi-restraints excluded: chain D residue 493 GLN Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 212 ASP Chi-restraints excluded: chain E residue 238 ASN Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 437 MET Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 312 ARG Chi-restraints excluded: chain F residue 414 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 209 optimal weight: 5.9990 chunk 220 optimal weight: 7.9990 chunk 201 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 65 optimal weight: 0.0570 chunk 193 optimal weight: 9.9990 chunk 203 optimal weight: 8.9990 chunk 213 optimal weight: 3.9990 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 GLN ** C 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN E 248 HIS E 438 ASN F 307 ASN F 318 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 21411 Z= 0.355 Angle : 0.580 8.984 29298 Z= 0.312 Chirality : 0.043 0.168 3322 Planarity : 0.003 0.055 3392 Dihedral : 18.396 82.928 3557 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.47 % Allowed : 21.55 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.17), residues: 2283 helix: 1.22 (0.15), residues: 1293 sheet: 0.35 (0.33), residues: 200 loop : -0.25 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 526 HIS 0.006 0.001 HIS C 62 PHE 0.018 0.001 PHE C 408 TYR 0.022 0.002 TYR F 306 ARG 0.005 0.000 ARG A 503 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 187 time to evaluate : 2.667 Fit side-chains REVERT: A 518 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.8032 (mtm) REVERT: A 859 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7624 (tt0) REVERT: B 448 ARG cc_start: 0.9309 (OUTLIER) cc_final: 0.8759 (mmm160) REVERT: C 454 HIS cc_start: 0.7686 (t70) cc_final: 0.7375 (t70) REVERT: C 592 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7977 (tm-30) REVERT: D 54 ARG cc_start: 0.8174 (ttm110) cc_final: 0.7842 (ttm110) REVERT: D 186 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9212 (mp) REVERT: E 212 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.8139 (t0) REVERT: E 217 LYS cc_start: 0.7737 (mmpt) cc_final: 0.7057 (mttm) REVERT: E 245 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8266 (mp10) REVERT: E 277 ASN cc_start: 0.7836 (m-40) cc_final: 0.7543 (m-40) REVERT: E 437 MET cc_start: 0.7041 (OUTLIER) cc_final: 0.6824 (pmm) REVERT: E 441 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.7972 (tp) REVERT: F 277 TYR cc_start: 0.8259 (m-80) cc_final: 0.7633 (m-80) REVERT: F 312 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7980 (ptt180) outliers start: 53 outliers final: 33 residues processed: 229 average time/residue: 1.5814 time to fit residues: 406.9947 Evaluate side-chains 224 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 181 time to evaluate : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain D residue 453 LYS Chi-restraints excluded: chain D residue 454 LYS Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 491 GLN Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 212 ASP Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 437 MET Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 312 ARG Chi-restraints excluded: chain F residue 414 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 140 optimal weight: 2.9990 chunk 226 optimal weight: 7.9990 chunk 138 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 chunk 157 optimal weight: 2.9990 chunk 238 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 chunk 189 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 271 ASN E 2 ASN E 438 ASN F 307 ASN F 318 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21411 Z= 0.223 Angle : 0.545 9.193 29298 Z= 0.292 Chirality : 0.041 0.174 3322 Planarity : 0.003 0.066 3392 Dihedral : 18.162 88.530 3557 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.96 % Allowed : 22.11 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.18), residues: 2283 helix: 1.41 (0.15), residues: 1277 sheet: 0.31 (0.33), residues: 200 loop : -0.15 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 494 HIS 0.005 0.001 HIS C 69 PHE 0.032 0.001 PHE C 412 TYR 0.021 0.001 TYR F 306 ARG 0.017 0.000 ARG B 271 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 185 time to evaluate : 2.551 Fit side-chains REVERT: A 518 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.8048 (mtm) REVERT: A 859 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7605 (tt0) REVERT: C 592 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7955 (tm-30) REVERT: D 186 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9198 (mp) REVERT: E 212 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.8170 (t0) REVERT: E 217 LYS cc_start: 0.7804 (mmpt) cc_final: 0.7158 (mttm) REVERT: E 245 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8278 (mp10) REVERT: E 277 ASN cc_start: 0.7760 (m-40) cc_final: 0.7482 (m-40) REVERT: E 441 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.7961 (tp) REVERT: F 277 TYR cc_start: 0.8255 (m-80) cc_final: 0.7637 (m-80) REVERT: F 312 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.8011 (ptt180) outliers start: 42 outliers final: 31 residues processed: 218 average time/residue: 1.6782 time to fit residues: 409.2708 Evaluate side-chains 219 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 180 time to evaluate : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain D residue 453 LYS Chi-restraints excluded: chain D residue 454 LYS Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 491 GLN Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 212 ASP Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 312 ARG Chi-restraints excluded: chain F residue 414 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 150 optimal weight: 8.9990 chunk 201 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 189 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 195 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 GLN E 2 ASN F 307 ASN F 318 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.096329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.070422 restraints weight = 36967.116| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.03 r_work: 0.2827 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21411 Z= 0.194 Angle : 0.532 9.110 29298 Z= 0.286 Chirality : 0.040 0.175 3322 Planarity : 0.003 0.061 3392 Dihedral : 18.011 87.326 3557 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.82 % Allowed : 22.43 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.18), residues: 2283 helix: 1.47 (0.15), residues: 1280 sheet: 0.30 (0.33), residues: 200 loop : -0.13 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 494 HIS 0.005 0.001 HIS C 69 PHE 0.018 0.001 PHE C 408 TYR 0.020 0.001 TYR F 306 ARG 0.010 0.000 ARG F 341 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7646.22 seconds wall clock time: 140 minutes 16.92 seconds (8416.92 seconds total)