Starting phenix.real_space_refine on Tue May 20 13:44:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zp4_60326/05_2025/8zp4_60326.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zp4_60326/05_2025/8zp4_60326.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zp4_60326/05_2025/8zp4_60326.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zp4_60326/05_2025/8zp4_60326.map" model { file = "/net/cci-nas-00/data/ceres_data/8zp4_60326/05_2025/8zp4_60326.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zp4_60326/05_2025/8zp4_60326.cif" } resolution = 3.33 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= 0.002 sd= 0.036 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 71 5.49 5 Mg 3 5.21 5 S 82 5.16 5 C 12657 2.51 5 N 3342 2.21 5 O 3874 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20029 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3955 Classifications: {'peptide': 494} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 484} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2958 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 348} Chain breaks: 3 Chain: "C" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4622 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 15, 'TRANS': 541} Chain breaks: 2 Chain: "D" Number of atoms: 3572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3572 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 425} Chain breaks: 3 Chain: "G" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "H" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 637 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "E" Number of atoms: 3555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3555 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 413} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 10.90, per 1000 atoms: 0.54 Number of scatterers: 20029 At special positions: 0 Unit cell: (104.94, 130.38, 167.48, 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 82 16.00 P 71 15.00 Mg 3 11.99 O 3874 8.00 N 3342 7.00 C 12657 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.07 Conformation dependent library (CDL) restraints added in 2.7 seconds 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4434 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 12 sheets defined 59.5% alpha, 7.0% beta 4 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 6.21 Creating SS restraints... Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 400 through 408 removed outlier: 3.905A pdb=" N SER A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 430 removed outlier: 4.083A pdb=" N LYS A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 469 Processing helix chain 'A' and resid 484 through 502 Processing helix chain 'A' and resid 520 through 522 No H-bonds generated for 'chain 'A' and resid 520 through 522' Processing helix chain 'A' and resid 523 through 533 Processing helix chain 'A' and resid 538 through 552 Processing helix chain 'A' and resid 554 through 558 removed outlier: 3.754A pdb=" N LYS A 558 " --> pdb=" O LYS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 573 removed outlier: 3.938A pdb=" N MET A 571 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR A 573 " --> pdb=" O ASP A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 585 Processing helix chain 'A' and resid 603 through 610 Processing helix chain 'A' and resid 610 through 617 Processing helix chain 'A' and resid 628 through 640 Processing helix chain 'A' and resid 685 through 698 Processing helix chain 'A' and resid 702 through 726 Processing helix chain 'A' and resid 774 through 787 Processing helix chain 'A' and resid 789 through 795 removed outlier: 3.740A pdb=" N THR A 795 " --> pdb=" O ILE A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 816 Processing helix chain 'A' and resid 822 through 836 removed outlier: 3.661A pdb=" N ASN A 836 " --> pdb=" O LEU A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 851 removed outlier: 4.569A pdb=" N LYS A 847 " --> pdb=" O MET A 843 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR A 848 " --> pdb=" O GLU A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 876 Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.671A pdb=" N ALA A 901 " --> pdb=" O SER A 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 Processing helix chain 'B' and resid 270 through 283 Processing helix chain 'B' and resid 286 through 299 removed outlier: 3.802A pdb=" N LYS B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 309 Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 333 through 343 removed outlier: 3.539A pdb=" N LEU B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 383 Processing helix chain 'B' and resid 389 through 394 removed outlier: 4.064A pdb=" N LYS B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 412 Processing helix chain 'B' and resid 434 through 446 removed outlier: 3.867A pdb=" N VAL B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 465 Processing helix chain 'B' and resid 466 through 474 Processing helix chain 'B' and resid 488 through 493 removed outlier: 3.745A pdb=" N PHE B 492 " --> pdb=" O GLU B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 516 removed outlier: 4.523A pdb=" N SER B 516 " --> pdb=" O TYR B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 539 Processing helix chain 'B' and resid 549 through 553 Processing helix chain 'B' and resid 556 through 566 Processing helix chain 'B' and resid 571 through 585 removed outlier: 4.156A pdb=" N GLU B 581 " --> pdb=" O SER B 577 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 616 Processing helix chain 'C' and resid 16 through 20 Processing helix chain 'C' and resid 43 through 48 Processing helix chain 'C' and resid 50 through 93 removed outlier: 3.548A pdb=" N VAL C 54 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR C 92 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 159 Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 190 through 196 Processing helix chain 'C' and resid 212 through 225 removed outlier: 3.529A pdb=" N LEU C 216 " --> pdb=" O ASN C 212 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 228 No H-bonds generated for 'chain 'C' and resid 226 through 228' Processing helix chain 'C' and resid 243 through 251 removed outlier: 4.151A pdb=" N ILE C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.831A pdb=" N ARG C 261 " --> pdb=" O ARG C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 289 Processing helix chain 'C' and resid 295 through 308 Processing helix chain 'C' and resid 313 through 332 Processing helix chain 'C' and resid 333 through 338 removed outlier: 3.772A pdb=" N VAL C 336 " --> pdb=" O ALA C 333 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C 338 " --> pdb=" O SER C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 346 removed outlier: 4.457A pdb=" N ASP C 344 " --> pdb=" O VAL C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 355 Processing helix chain 'C' and resid 357 through 363 Processing helix chain 'C' and resid 390 through 394 Processing helix chain 'C' and resid 400 through 416 removed outlier: 4.695A pdb=" N GLY C 404 " --> pdb=" O ASN C 400 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU C 416 " --> pdb=" O PHE C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 434 Processing helix chain 'C' and resid 435 through 441 removed outlier: 3.535A pdb=" N TYR C 439 " --> pdb=" O LYS C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 480 removed outlier: 3.542A pdb=" N ILE C 479 " --> pdb=" O LEU C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 493 Processing helix chain 'C' and resid 494 through 497 Processing helix chain 'C' and resid 512 through 517 removed outlier: 4.219A pdb=" N ILE C 516 " --> pdb=" O ASP C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 530 removed outlier: 3.582A pdb=" N LEU C 527 " --> pdb=" O GLN C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 548 Processing helix chain 'C' and resid 550 through 559 removed outlier: 3.551A pdb=" N LEU C 554 " --> pdb=" O LYS C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 571 removed outlier: 3.530A pdb=" N GLU C 571 " --> pdb=" O LEU C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 595 removed outlier: 3.582A pdb=" N LEU C 581 " --> pdb=" O ASP C 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 75 through 91 Processing helix chain 'D' and resid 108 through 121 Processing helix chain 'D' and resid 138 through 158 removed outlier: 4.389A pdb=" N ILE D 143 " --> pdb=" O GLU D 139 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN D 144 " --> pdb=" O GLN D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 189 Processing helix chain 'D' and resid 218 through 224 removed outlier: 4.364A pdb=" N PHE D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY D 224 " --> pdb=" O ASP D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 241 Processing helix chain 'D' and resid 255 through 259 Processing helix chain 'D' and resid 261 through 268 Processing helix chain 'D' and resid 280 through 293 Processing helix chain 'D' and resid 301 through 313 removed outlier: 4.087A pdb=" N GLU D 307 " --> pdb=" O SER D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 331 Processing helix chain 'D' and resid 333 through 348 removed outlier: 3.629A pdb=" N LEU D 337 " --> pdb=" O SER D 333 " (cutoff:3.500A) Proline residue: D 343 - end of helix removed outlier: 4.028A pdb=" N SER D 348 " --> pdb=" O LEU D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 361 Processing helix chain 'D' and resid 361 through 372 Processing helix chain 'D' and resid 376 through 381 Processing helix chain 'D' and resid 384 through 401 Processing helix chain 'D' and resid 407 through 426 Processing helix chain 'D' and resid 452 through 466 removed outlier: 4.559A pdb=" N ASN D 458 " --> pdb=" O LYS D 454 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL D 459 " --> pdb=" O ASP D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 490 Processing helix chain 'D' and resid 492 through 497 removed outlier: 3.975A pdb=" N MET D 496 " --> pdb=" O PHE D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 517 Processing helix chain 'E' and resid 11 through 22 Processing helix chain 'E' and resid 25 through 29 removed outlier: 3.719A pdb=" N THR E 29 " --> pdb=" O PRO E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 54 Processing helix chain 'E' and resid 69 through 89 removed outlier: 3.672A pdb=" N LEU E 73 " --> pdb=" O SER E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 102 removed outlier: 3.801A pdb=" N VAL E 102 " --> pdb=" O PRO E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 118 removed outlier: 3.635A pdb=" N GLN E 118 " --> pdb=" O ASN E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 138 removed outlier: 3.505A pdb=" N LEU E 138 " --> pdb=" O PHE E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 152 removed outlier: 3.617A pdb=" N TYR E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 155 No H-bonds generated for 'chain 'E' and resid 153 through 155' Processing helix chain 'E' and resid 174 through 179 removed outlier: 3.828A pdb=" N ARG E 178 " --> pdb=" O SER E 174 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TYR E 179 " --> pdb=" O PHE E 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 174 through 179' Processing helix chain 'E' and resid 180 through 183 removed outlier: 3.668A pdb=" N CYS E 183 " --> pdb=" O SER E 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 180 through 183' Processing helix chain 'E' and resid 193 through 211 removed outlier: 5.330A pdb=" N GLY E 207 " --> pdb=" O MET E 203 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLU E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 223 Processing helix chain 'E' and resid 228 through 252 removed outlier: 5.750A pdb=" N SER E 249 " --> pdb=" O GLN E 245 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TYR E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 272 Proline residue: E 267 - end of helix Processing helix chain 'E' and resid 274 through 279 removed outlier: 4.476A pdb=" N PHE E 279 " --> pdb=" O LYS E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 288 removed outlier: 3.897A pdb=" N LEU E 284 " --> pdb=" O GLU E 280 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR E 285 " --> pdb=" O PRO E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 340 Processing helix chain 'E' and resid 342 through 344 No H-bonds generated for 'chain 'E' and resid 342 through 344' Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 372 through 376 Processing helix chain 'E' and resid 382 through 394 Processing helix chain 'E' and resid 417 through 430 Processing helix chain 'E' and resid 455 through 467 removed outlier: 3.537A pdb=" N ILE E 459 " --> pdb=" O PRO E 455 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 508 through 512 removed outlier: 6.822A pdb=" N ILE A 561 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ILE A 596 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL A 563 " --> pdb=" O ILE A 596 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL A 598 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU A 565 " --> pdb=" O VAL A 598 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 657 through 659 removed outlier: 7.479A pdb=" N GLN A 771 " --> pdb=" O LYS A 679 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ARG A 681 " --> pdb=" O GLN A 771 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 820 through 821 Processing sheet with id=AA4, first strand: chain 'B' and resid 476 through 479 removed outlier: 3.606A pdb=" N LEU B 315 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU B 314 " --> pdb=" O ALA B 454 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N THR B 456 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE B 316 " --> pdb=" O THR B 456 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 453 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU B 361 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N HIS B 425 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU B 363 " --> pdb=" O HIS B 425 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE B 362 " --> pdb=" O TYR C 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 554 through 555 Processing sheet with id=AA6, first strand: chain 'C' and resid 124 through 131 removed outlier: 6.246A pdb=" N TYR C 125 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL C 202 " --> pdb=" O TYR C 125 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL C 127 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ASN C 204 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE C 129 " --> pdb=" O ASN C 204 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASN C 103 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE C 238 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE C 105 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR C 104 " --> pdb=" O HIS C 264 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU C 266 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N PHE C 106 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 534 through 536 Processing sheet with id=AA8, first strand: chain 'D' and resid 127 through 133 removed outlier: 6.615A pdb=" N VAL D 212 " --> pdb=" O CYS D 246 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N PHE D 248 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N PHE D 214 " --> pdb=" O PHE D 248 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N CYS D 250 " --> pdb=" O PHE D 214 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE D 216 " --> pdb=" O CYS D 250 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N HIS D 96 " --> pdb=" O ILE D 247 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N GLY D 249 " --> pdb=" O HIS D 96 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL D 98 " --> pdb=" O GLY D 249 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N THR D 251 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N LEU D 100 " --> pdb=" O THR D 251 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N ILE D 273 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE D 99 " --> pdb=" O ILE D 273 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 469 through 471 Processing sheet with id=AB1, first strand: chain 'E' and resid 34 through 37 removed outlier: 6.434A pdb=" N ILE E 34 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE E 189 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLN E 36 " --> pdb=" O PHE E 189 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 62 removed outlier: 4.639A pdb=" N HIS E 58 " --> pdb=" O CYS E 127 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 433 through 435 908 hydrogen bonds defined for protein. 2622 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 6.70 Time building geometry restraints manager: 5.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 6245 1.35 - 1.50: 5736 1.50 - 1.64: 8439 1.64 - 1.78: 5 1.78 - 1.92: 133 Bond restraints: 20558 Sorted by residual: bond pdb=" O2B AGS D2001 " pdb=" PB AGS D2001 " ideal model delta sigma weight residual 1.531 1.469 0.062 1.60e-02 3.91e+03 1.51e+01 bond pdb=" O2B AGS E 502 " pdb=" PB AGS E 502 " ideal model delta sigma weight residual 1.531 1.469 0.062 1.60e-02 3.91e+03 1.50e+01 bond pdb=" O3G AGS D2001 " pdb=" PG AGS D2001 " ideal model delta sigma weight residual 1.558 1.486 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" O2B AGS A2001 " pdb=" PB AGS A2001 " ideal model delta sigma weight residual 1.531 1.475 0.056 1.60e-02 3.91e+03 1.23e+01 bond pdb=" O2G AGS A2001 " pdb=" PG AGS A2001 " ideal model delta sigma weight residual 1.557 1.490 0.067 2.00e-02 2.50e+03 1.13e+01 ... (remaining 20553 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 27516 1.77 - 3.55: 439 3.55 - 5.32: 69 5.32 - 7.09: 23 7.09 - 8.86: 13 Bond angle restraints: 28060 Sorted by residual: angle pdb=" O3A AGS D2001 " pdb=" PB AGS D2001 " pdb=" O3B AGS D2001 " ideal model delta sigma weight residual 109.69 100.83 8.86 3.00e+00 1.11e-01 8.73e+00 angle pdb=" C GLU E 172 " pdb=" N THR E 173 " pdb=" CA THR E 173 " ideal model delta sigma weight residual 121.54 127.12 -5.58 1.91e+00 2.74e-01 8.54e+00 angle pdb=" O3B AGS E 502 " pdb=" PG AGS E 502 " pdb=" O3G AGS E 502 " ideal model delta sigma weight residual 109.43 100.82 8.61 3.00e+00 1.11e-01 8.24e+00 angle pdb=" N GLY C 290 " pdb=" CA GLY C 290 " pdb=" C GLY C 290 " ideal model delta sigma weight residual 115.62 110.92 4.70 1.71e+00 3.42e-01 7.55e+00 angle pdb=" O2G AGS A2001 " pdb=" PG AGS A2001 " pdb=" O3B AGS A2001 " ideal model delta sigma weight residual 109.53 101.46 8.07 3.00e+00 1.11e-01 7.24e+00 ... (remaining 28055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.84: 11581 29.84 - 59.69: 698 59.69 - 89.53: 31 89.53 - 119.38: 1 119.38 - 149.22: 1 Dihedral angle restraints: 12312 sinusoidal: 5514 harmonic: 6798 Sorted by residual: dihedral pdb=" O1A AGS E 502 " pdb=" O3A AGS E 502 " pdb=" PA AGS E 502 " pdb=" PB AGS E 502 " ideal model delta sinusoidal sigma weight residual -67.73 81.49 -149.22 1 3.00e+01 1.11e-03 1.98e+01 dihedral pdb=" O1A AGS A2001 " pdb=" O3A AGS A2001 " pdb=" PA AGS A2001 " pdb=" PB AGS A2001 " ideal model delta sinusoidal sigma weight residual -67.73 48.22 -115.95 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" CA THR E 173 " pdb=" C THR E 173 " pdb=" N SER E 174 " pdb=" CA SER E 174 " ideal model delta harmonic sigma weight residual 180.00 160.61 19.39 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 12309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2589 0.051 - 0.102: 505 0.102 - 0.153: 82 0.153 - 0.204: 4 0.204 - 0.255: 1 Chirality restraints: 3181 Sorted by residual: chirality pdb=" CB ILE D 247 " pdb=" CA ILE D 247 " pdb=" CG1 ILE D 247 " pdb=" CG2 ILE D 247 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CB THR C 113 " pdb=" CA THR C 113 " pdb=" OG1 THR C 113 " pdb=" CG2 THR C 113 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.37e-01 chirality pdb=" CB ILE A 578 " pdb=" CA ILE A 578 " pdb=" CG1 ILE A 578 " pdb=" CG2 ILE A 578 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.75e-01 ... (remaining 3178 not shown) Planarity restraints: 3312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 136 " -0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO C 137 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 137 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 137 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 334 " 0.025 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO D 335 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO D 335 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 335 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 202 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.92e+00 pdb=" C VAL E 202 " -0.024 2.00e-02 2.50e+03 pdb=" O VAL E 202 " 0.009 2.00e-02 2.50e+03 pdb=" N MET E 203 " 0.008 2.00e-02 2.50e+03 ... (remaining 3309 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1899 2.74 - 3.28: 20455 3.28 - 3.82: 33570 3.82 - 4.36: 39237 4.36 - 4.90: 66879 Nonbonded interactions: 162040 Sorted by model distance: nonbonded pdb=" ND2 ASN A 886 " pdb=" OE1 GLN D 507 " model vdw 2.203 3.120 nonbonded pdb=" OH TYR C 229 " pdb=" OE1 GLU E 66 " model vdw 2.230 3.040 nonbonded pdb=" OD1 ASP C 217 " pdb=" OG1 THR C 255 " model vdw 2.236 3.040 nonbonded pdb=" OG SER C 50 " pdb=" OD1 ASN C 53 " model vdw 2.239 3.040 nonbonded pdb=" O3G AGS A2001 " pdb="MG MG A2002 " model vdw 2.249 2.170 ... (remaining 162035 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 47.330 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 20558 Z= 0.175 Angle : 0.597 8.864 28060 Z= 0.300 Chirality : 0.041 0.255 3181 Planarity : 0.003 0.050 3312 Dihedral : 17.009 149.220 7878 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.18), residues: 2248 helix: 1.32 (0.16), residues: 1183 sheet: -0.35 (0.36), residues: 193 loop : -1.03 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 58 HIS 0.006 0.001 HIS C 69 PHE 0.022 0.001 PHE B 475 TYR 0.017 0.001 TYR E 336 ARG 0.007 0.000 ARG B 250 Details of bonding type rmsd hydrogen bonds : bond 0.14911 ( 918) hydrogen bonds : angle 5.86300 ( 2642) covalent geometry : bond 0.00385 (20558) covalent geometry : angle 0.59653 (28060) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 465 LEU cc_start: 0.8840 (pp) cc_final: 0.8291 (pp) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.3368 time to fit residues: 60.7803 Evaluate side-chains 74 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 2.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.9990 chunk 175 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 118 optimal weight: 0.0060 chunk 93 optimal weight: 8.9990 chunk 181 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 chunk 210 optimal weight: 10.0000 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 GLN B 538 ASN D 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.062437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.043063 restraints weight = 83531.817| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 3.90 r_work: 0.2681 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20558 Z= 0.157 Angle : 0.562 7.953 28060 Z= 0.300 Chirality : 0.041 0.152 3181 Planarity : 0.003 0.039 3312 Dihedral : 16.605 144.477 3233 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.34 % Favored : 96.62 % Rotamer: Outliers : 0.33 % Allowed : 6.82 % Favored : 92.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.50 (0.18), residues: 2248 helix: 1.38 (0.15), residues: 1201 sheet: -0.58 (0.35), residues: 197 loop : -0.92 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 526 HIS 0.009 0.001 HIS A 416 PHE 0.018 0.001 PHE C 334 TYR 0.014 0.001 TYR B 372 ARG 0.005 0.000 ARG C 411 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 918) hydrogen bonds : angle 4.56354 ( 2642) covalent geometry : bond 0.00356 (20558) covalent geometry : angle 0.56248 (28060) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 2.522 Fit side-chains revert: symmetry clash REVERT: A 722 MET cc_start: 0.8592 (mtm) cc_final: 0.8213 (mtm) REVERT: B 263 MET cc_start: 0.8302 (mmp) cc_final: 0.8004 (mmm) REVERT: C 285 LEU cc_start: 0.9664 (tp) cc_final: 0.9377 (tt) REVERT: D 506 MET cc_start: 0.8840 (tpp) cc_final: 0.8585 (mmm) REVERT: E 140 ASP cc_start: 0.8977 (t70) cc_final: 0.8638 (t0) outliers start: 7 outliers final: 2 residues processed: 86 average time/residue: 0.3188 time to fit residues: 45.5020 Evaluate side-chains 73 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain B residue 549 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 198 optimal weight: 0.8980 chunk 116 optimal weight: 20.0000 chunk 160 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN E 423 ASN E 467 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.062241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.042577 restraints weight = 83445.536| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 3.93 r_work: 0.2675 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20558 Z= 0.142 Angle : 0.525 8.476 28060 Z= 0.279 Chirality : 0.040 0.145 3181 Planarity : 0.003 0.039 3312 Dihedral : 16.565 137.163 3233 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.95 % Allowed : 10.01 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.69 (0.18), residues: 2248 helix: 1.55 (0.16), residues: 1203 sheet: -0.46 (0.35), residues: 197 loop : -0.89 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 58 HIS 0.011 0.001 HIS E 467 PHE 0.017 0.001 PHE C 334 TYR 0.015 0.001 TYR A 580 ARG 0.004 0.000 ARG C 452 Details of bonding type rmsd hydrogen bonds : bond 0.03316 ( 918) hydrogen bonds : angle 4.29603 ( 2642) covalent geometry : bond 0.00321 (20558) covalent geometry : angle 0.52543 (28060) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 2.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 722 MET cc_start: 0.8509 (mtm) cc_final: 0.8060 (mtm) REVERT: B 263 MET cc_start: 0.8328 (mmp) cc_final: 0.8026 (mmm) REVERT: D 188 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8540 (tp) REVERT: E 140 ASP cc_start: 0.8970 (t70) cc_final: 0.8659 (t0) outliers start: 20 outliers final: 7 residues processed: 94 average time/residue: 0.2855 time to fit residues: 45.4654 Evaluate side-chains 80 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain E residue 170 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 22 optimal weight: 0.6980 chunk 151 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 195 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 205 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 GLN B 538 ASN D 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.062221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.042930 restraints weight = 84035.366| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 3.87 r_work: 0.2677 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20558 Z= 0.137 Angle : 0.513 8.523 28060 Z= 0.274 Chirality : 0.039 0.157 3181 Planarity : 0.003 0.038 3312 Dihedral : 16.518 134.603 3233 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.19 % Allowed : 10.87 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.77 (0.18), residues: 2248 helix: 1.68 (0.16), residues: 1197 sheet: -0.46 (0.35), residues: 195 loop : -0.92 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 526 HIS 0.004 0.001 HIS C 69 PHE 0.024 0.001 PHE C 395 TYR 0.014 0.001 TYR A 580 ARG 0.002 0.000 ARG B 250 Details of bonding type rmsd hydrogen bonds : bond 0.03054 ( 918) hydrogen bonds : angle 4.16438 ( 2642) covalent geometry : bond 0.00309 (20558) covalent geometry : angle 0.51274 (28060) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 2.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 602 MET cc_start: 0.8836 (tpp) cc_final: 0.7987 (tpp) REVERT: A 623 MET cc_start: 0.9151 (tpt) cc_final: 0.8773 (tpp) REVERT: B 263 MET cc_start: 0.8347 (mmp) cc_final: 0.8024 (mmm) REVERT: D 188 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8853 (tt) REVERT: E 140 ASP cc_start: 0.8975 (t70) cc_final: 0.8662 (t0) REVERT: E 414 MET cc_start: 0.8383 (tpt) cc_final: 0.8156 (tpt) outliers start: 25 outliers final: 8 residues processed: 96 average time/residue: 0.2797 time to fit residues: 45.2734 Evaluate side-chains 82 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain E residue 170 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 134 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 198 optimal weight: 0.7980 chunk 127 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 GLN ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.061387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.041573 restraints weight = 85193.492| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 3.99 r_work: 0.2609 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20558 Z= 0.186 Angle : 0.540 8.589 28060 Z= 0.284 Chirality : 0.040 0.149 3181 Planarity : 0.003 0.038 3312 Dihedral : 16.613 135.887 3233 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.33 % Allowed : 11.73 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.18), residues: 2248 helix: 1.71 (0.16), residues: 1209 sheet: -0.50 (0.35), residues: 197 loop : -0.89 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 526 HIS 0.005 0.001 HIS C 69 PHE 0.020 0.001 PHE C 334 TYR 0.017 0.001 TYR A 580 ARG 0.002 0.000 ARG E 344 Details of bonding type rmsd hydrogen bonds : bond 0.03116 ( 918) hydrogen bonds : angle 4.11407 ( 2642) covalent geometry : bond 0.00422 (20558) covalent geometry : angle 0.54011 (28060) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 560 THR cc_start: 0.8012 (OUTLIER) cc_final: 0.7695 (p) REVERT: A 579 MET cc_start: 0.8301 (tmm) cc_final: 0.7873 (tmm) REVERT: B 263 MET cc_start: 0.8543 (mmp) cc_final: 0.8208 (mmm) REVERT: C 71 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8703 (mp10) REVERT: C 285 LEU cc_start: 0.9722 (tp) cc_final: 0.9395 (tt) REVERT: C 361 MET cc_start: 0.8900 (tpp) cc_final: 0.8275 (mmm) REVERT: C 585 MET cc_start: 0.9279 (tpt) cc_final: 0.9071 (tpt) REVERT: D 188 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8822 (tt) REVERT: D 506 MET cc_start: 0.9134 (tpp) cc_final: 0.8730 (tmm) REVERT: E 140 ASP cc_start: 0.9020 (t70) cc_final: 0.8702 (t0) REVERT: E 414 MET cc_start: 0.8235 (tpt) cc_final: 0.8021 (tpt) outliers start: 28 outliers final: 13 residues processed: 98 average time/residue: 0.3188 time to fit residues: 51.0850 Evaluate side-chains 89 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 2.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 437 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 201 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 129 optimal weight: 0.1980 chunk 140 optimal weight: 0.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.061152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.041236 restraints weight = 84526.354| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 4.00 r_work: 0.2608 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20558 Z= 0.180 Angle : 0.539 8.935 28060 Z= 0.283 Chirality : 0.040 0.196 3181 Planarity : 0.003 0.038 3312 Dihedral : 16.619 135.451 3233 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.14 % Allowed : 12.96 % Favored : 85.89 % 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: 0.87 (0.18), residues: 2248 helix: 1.74 (0.15), residues: 1209 sheet: -0.47 (0.35), residues: 197 loop : -0.86 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 58 HIS 0.005 0.001 HIS C 69 PHE 0.016 0.001 PHE C 334 TYR 0.016 0.001 TYR A 580 ARG 0.003 0.000 ARG A 503 Details of bonding type rmsd hydrogen bonds : bond 0.03040 ( 918) hydrogen bonds : angle 4.06951 ( 2642) covalent geometry : bond 0.00408 (20558) covalent geometry : angle 0.53864 (28060) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 2.506 Fit side-chains revert: symmetry clash REVERT: A 485 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7987 (ptpp) REVERT: A 560 THR cc_start: 0.8030 (OUTLIER) cc_final: 0.7710 (p) REVERT: A 579 MET cc_start: 0.8351 (tmm) cc_final: 0.8027 (tmm) REVERT: A 623 MET cc_start: 0.9129 (tpt) cc_final: 0.8916 (tpt) REVERT: B 263 MET cc_start: 0.8677 (mmp) cc_final: 0.8364 (mmm) REVERT: C 285 LEU cc_start: 0.9734 (tp) cc_final: 0.9406 (tt) REVERT: C 361 MET cc_start: 0.8930 (tpp) cc_final: 0.8284 (mmm) REVERT: D 188 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8786 (tt) REVERT: D 506 MET cc_start: 0.9124 (tpp) cc_final: 0.8651 (tmm) REVERT: E 140 ASP cc_start: 0.9030 (t70) cc_final: 0.8711 (t0) REVERT: E 414 MET cc_start: 0.8235 (tpt) cc_final: 0.7964 (tpt) outliers start: 24 outliers final: 18 residues processed: 97 average time/residue: 0.3112 time to fit residues: 50.8216 Evaluate side-chains 92 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 437 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 51 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 15 optimal weight: 0.0170 chunk 147 optimal weight: 1.9990 chunk 129 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 GLN ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.060813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.041012 restraints weight = 84172.737| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.95 r_work: 0.2598 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20558 Z= 0.195 Angle : 0.557 11.551 28060 Z= 0.292 Chirality : 0.040 0.195 3181 Planarity : 0.003 0.038 3312 Dihedral : 16.697 136.195 3233 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.33 % Allowed : 13.82 % Favored : 84.84 % 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: 0.88 (0.18), residues: 2248 helix: 1.73 (0.15), residues: 1218 sheet: -0.49 (0.36), residues: 197 loop : -0.84 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 58 HIS 0.003 0.001 HIS E 428 PHE 0.028 0.001 PHE C 599 TYR 0.017 0.001 TYR A 580 ARG 0.002 0.000 ARG A 503 Details of bonding type rmsd hydrogen bonds : bond 0.03079 ( 918) hydrogen bonds : angle 4.06476 ( 2642) covalent geometry : bond 0.00443 (20558) covalent geometry : angle 0.55674 (28060) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 2.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 485 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7984 (ptpp) REVERT: A 560 THR cc_start: 0.8068 (OUTLIER) cc_final: 0.7750 (p) REVERT: A 579 MET cc_start: 0.8483 (tmm) cc_final: 0.8160 (tmm) REVERT: A 623 MET cc_start: 0.9157 (tpt) cc_final: 0.8931 (tpp) REVERT: B 263 MET cc_start: 0.8741 (mmp) cc_final: 0.8450 (mmm) REVERT: C 71 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8686 (mt0) REVERT: C 285 LEU cc_start: 0.9732 (tp) cc_final: 0.9406 (tt) REVERT: D 188 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8745 (tt) REVERT: D 506 MET cc_start: 0.9093 (tpp) cc_final: 0.8650 (mmm) REVERT: E 140 ASP cc_start: 0.9041 (t70) cc_final: 0.8726 (t0) REVERT: E 414 MET cc_start: 0.8201 (tpt) cc_final: 0.7930 (tpt) outliers start: 28 outliers final: 19 residues processed: 101 average time/residue: 0.2916 time to fit residues: 49.6637 Evaluate side-chains 96 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 194 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 191 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 167 optimal weight: 0.7980 chunk 162 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.061171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.041366 restraints weight = 84767.829| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 3.98 r_work: 0.2610 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20558 Z= 0.153 Angle : 0.536 11.712 28060 Z= 0.282 Chirality : 0.040 0.202 3181 Planarity : 0.003 0.038 3312 Dihedral : 16.662 134.988 3233 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.24 % Allowed : 14.20 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.18), residues: 2248 helix: 1.74 (0.15), residues: 1219 sheet: -0.44 (0.36), residues: 197 loop : -0.83 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 58 HIS 0.005 0.001 HIS C 69 PHE 0.072 0.001 PHE C 599 TYR 0.017 0.001 TYR C 605 ARG 0.002 0.000 ARG C 145 Details of bonding type rmsd hydrogen bonds : bond 0.02977 ( 918) hydrogen bonds : angle 4.00830 ( 2642) covalent geometry : bond 0.00351 (20558) covalent geometry : angle 0.53613 (28060) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 2.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 485 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8013 (ptpp) REVERT: A 579 MET cc_start: 0.8513 (tmm) cc_final: 0.8206 (tmm) REVERT: A 623 MET cc_start: 0.9146 (tpt) cc_final: 0.8933 (tpp) REVERT: B 263 MET cc_start: 0.8749 (mmp) cc_final: 0.8494 (mmm) REVERT: C 285 LEU cc_start: 0.9718 (tp) cc_final: 0.9384 (tt) REVERT: D 188 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8701 (tt) REVERT: E 140 ASP cc_start: 0.9046 (t70) cc_final: 0.8722 (t0) REVERT: E 414 MET cc_start: 0.8238 (tpt) cc_final: 0.7962 (tpt) outliers start: 26 outliers final: 19 residues processed: 97 average time/residue: 0.2699 time to fit residues: 44.4679 Evaluate side-chains 93 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain D residue 53 GLN Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 437 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 41 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 220 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 199 optimal weight: 0.9990 chunk 221 optimal weight: 7.9990 chunk 184 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.061077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.041228 restraints weight = 84839.756| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 3.99 r_work: 0.2603 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 20558 Z= 0.170 Angle : 0.542 10.841 28060 Z= 0.284 Chirality : 0.040 0.200 3181 Planarity : 0.003 0.038 3312 Dihedral : 16.687 135.384 3233 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.24 % Allowed : 14.44 % Favored : 84.32 % 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: 0.95 (0.18), residues: 2248 helix: 1.77 (0.15), residues: 1217 sheet: -0.40 (0.36), residues: 197 loop : -0.79 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 58 HIS 0.003 0.001 HIS E 428 PHE 0.047 0.001 PHE C 334 TYR 0.017 0.001 TYR C 605 ARG 0.003 0.000 ARG C 145 Details of bonding type rmsd hydrogen bonds : bond 0.02980 ( 918) hydrogen bonds : angle 3.98381 ( 2642) covalent geometry : bond 0.00389 (20558) covalent geometry : angle 0.54222 (28060) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 2.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 579 MET cc_start: 0.8543 (tmm) cc_final: 0.8233 (tmm) REVERT: A 792 THR cc_start: 0.9569 (OUTLIER) cc_final: 0.9312 (p) REVERT: C 285 LEU cc_start: 0.9717 (tp) cc_final: 0.9376 (tt) REVERT: D 188 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8662 (tt) REVERT: E 140 ASP cc_start: 0.9048 (t70) cc_final: 0.8726 (t0) outliers start: 26 outliers final: 21 residues processed: 96 average time/residue: 0.2827 time to fit residues: 45.8734 Evaluate side-chains 97 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 2.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain D residue 53 GLN Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 194 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 207 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 157 optimal weight: 0.4980 chunk 7 optimal weight: 0.4980 chunk 87 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.061316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.041642 restraints weight = 84392.483| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 3.96 r_work: 0.2615 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20558 Z= 0.153 Angle : 0.539 10.656 28060 Z= 0.282 Chirality : 0.039 0.192 3181 Planarity : 0.003 0.038 3312 Dihedral : 16.682 134.524 3233 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.24 % Allowed : 14.49 % Favored : 84.27 % 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: 1.00 (0.18), residues: 2248 helix: 1.81 (0.15), residues: 1217 sheet: -0.46 (0.35), residues: 207 loop : -0.75 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 58 HIS 0.003 0.001 HIS C 69 PHE 0.049 0.001 PHE C 334 TYR 0.016 0.001 TYR C 605 ARG 0.003 0.000 ARG C 145 Details of bonding type rmsd hydrogen bonds : bond 0.02914 ( 918) hydrogen bonds : angle 3.94476 ( 2642) covalent geometry : bond 0.00350 (20558) covalent geometry : angle 0.53893 (28060) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 2.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 579 MET cc_start: 0.8516 (tmm) cc_final: 0.8212 (tmm) REVERT: A 792 THR cc_start: 0.9564 (OUTLIER) cc_final: 0.9307 (p) REVERT: C 285 LEU cc_start: 0.9715 (tp) cc_final: 0.9370 (tt) REVERT: C 517 MET cc_start: 0.9270 (tmm) cc_final: 0.9047 (ppp) REVERT: D 188 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8655 (tt) REVERT: E 140 ASP cc_start: 0.9044 (t70) cc_final: 0.8723 (t0) REVERT: E 414 MET cc_start: 0.8123 (tpt) cc_final: 0.7857 (tpt) outliers start: 26 outliers final: 19 residues processed: 97 average time/residue: 0.2882 time to fit residues: 47.8613 Evaluate side-chains 94 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain D residue 53 GLN Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 194 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 112 optimal weight: 10.0000 chunk 142 optimal weight: 0.0270 chunk 66 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 89 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 214 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 203 optimal weight: 1.9990 overall best weight: 2.3044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.060681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.040955 restraints weight = 85279.854| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 3.97 r_work: 0.2593 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 20558 Z= 0.200 Angle : 0.559 9.787 28060 Z= 0.293 Chirality : 0.040 0.201 3181 Planarity : 0.003 0.038 3312 Dihedral : 16.794 136.474 3233 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.10 % Allowed : 14.73 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.18), residues: 2248 helix: 1.79 (0.15), residues: 1223 sheet: -0.47 (0.35), residues: 207 loop : -0.73 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 58 HIS 0.004 0.001 HIS B 478 PHE 0.049 0.001 PHE C 334 TYR 0.018 0.001 TYR A 580 ARG 0.006 0.000 ARG B 551 Details of bonding type rmsd hydrogen bonds : bond 0.03053 ( 918) hydrogen bonds : angle 3.98306 ( 2642) covalent geometry : bond 0.00454 (20558) covalent geometry : angle 0.55944 (28060) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9737.37 seconds wall clock time: 169 minutes 41.47 seconds (10181.47 seconds total)