Starting phenix.real_space_refine on Thu Sep 18 20:44:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zp4_60326/09_2025/8zp4_60326.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zp4_60326/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zp4_60326/09_2025/8zp4_60326.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zp4_60326/09_2025/8zp4_60326.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zp4_60326/09_2025/8zp4_60326.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zp4_60326/09_2025/8zp4_60326.map" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.29, per 1000 atoms: 0.21 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: 1.35 Conformation dependent library (CDL) restraints added in 634.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.18 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: 3.19 Time building geometry restraints manager: 1.80 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: 2.190 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.380 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.520 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.000 ARG B 250 TYR 0.017 0.001 TYR E 336 PHE 0.022 0.001 PHE B 475 TRP 0.014 0.001 TRP C 58 HIS 0.006 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00385 (20558) covalent geometry : angle 0.59653 (28060) hydrogen bonds : bond 0.14911 ( 918) hydrogen bonds : angle 5.86300 ( 2642) *********************** 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 : 0.709 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: 0.1472 time to fit residues: 26.5166 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 : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 0.4980 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0020 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.7980 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN ** A 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3431 r_free = 0.3431 target = 0.062902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.043362 restraints weight = 83207.907| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 3.94 r_work: 0.2695 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20558 Z= 0.133 Angle : 0.551 7.683 28060 Z= 0.294 Chirality : 0.040 0.149 3181 Planarity : 0.003 0.039 3312 Dihedral : 16.542 144.501 3233 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.29 % Favored : 96.66 % Rotamer: Outliers : 0.33 % Allowed : 6.72 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.18), residues: 2248 helix: 1.37 (0.15), residues: 1206 sheet: -0.53 (0.35), residues: 197 loop : -0.91 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 411 TYR 0.012 0.001 TYR B 372 PHE 0.018 0.001 PHE C 334 TRP 0.022 0.001 TRP D 526 HIS 0.010 0.001 HIS A 416 Details of bonding type rmsd covalent geometry : bond 0.00297 (20558) covalent geometry : angle 0.55136 (28060) hydrogen bonds : bond 0.03950 ( 918) hydrogen bonds : angle 4.57908 ( 2642) *********************** 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 91 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: A 579 MET cc_start: 0.8547 (ttt) cc_final: 0.8175 (tmm) REVERT: A 722 MET cc_start: 0.8576 (mtm) cc_final: 0.8196 (mtm) REVERT: B 263 MET cc_start: 0.8365 (mmp) cc_final: 0.8079 (mmm) REVERT: C 285 LEU cc_start: 0.9660 (tp) cc_final: 0.9374 (tt) REVERT: C 331 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.8108 (mp10) REVERT: D 506 MET cc_start: 0.8798 (tpp) cc_final: 0.8550 (mmm) REVERT: E 140 ASP cc_start: 0.8967 (t70) cc_final: 0.8630 (t0) outliers start: 7 outliers final: 2 residues processed: 87 average time/residue: 0.1365 time to fit residues: 19.6399 Evaluate side-chains 75 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain C residue 331 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 151 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 128 optimal weight: 0.0870 chunk 83 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 158 optimal weight: 6.9990 chunk 226 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 493 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 = 0.3434 r_free = 0.3434 target = 0.063017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.043606 restraints weight = 83456.752| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 3.93 r_work: 0.2704 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 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 0.035 20558 Z= 0.117 Angle : 0.512 8.221 28060 Z= 0.272 Chirality : 0.039 0.145 3181 Planarity : 0.003 0.039 3312 Dihedral : 16.507 136.252 3233 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.95 % Allowed : 9.58 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.18), residues: 2248 helix: 1.52 (0.15), residues: 1202 sheet: -0.49 (0.35), residues: 197 loop : -0.85 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 272 TYR 0.011 0.001 TYR B 372 PHE 0.025 0.001 PHE C 334 TRP 0.012 0.001 TRP C 58 HIS 0.013 0.001 HIS E 467 Details of bonding type rmsd covalent geometry : bond 0.00258 (20558) covalent geometry : angle 0.51185 (28060) hydrogen bonds : bond 0.03250 ( 918) hydrogen bonds : angle 4.29678 ( 2642) *********************** 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 102 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 722 MET cc_start: 0.8497 (mtm) cc_final: 0.8062 (mtm) REVERT: B 263 MET cc_start: 0.8280 (mmp) cc_final: 0.8034 (mmm) REVERT: C 306 MET cc_start: 0.9010 (tmm) cc_final: 0.8803 (tmm) REVERT: C 331 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.8106 (mp10) REVERT: D 188 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8564 (tp) REVERT: E 140 ASP cc_start: 0.8967 (t70) cc_final: 0.8637 (t0) outliers start: 20 outliers final: 5 residues processed: 100 average time/residue: 0.1245 time to fit residues: 20.9807 Evaluate side-chains 82 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 497 ILE 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 141 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 86 optimal weight: 0.0870 chunk 68 optimal weight: 7.9990 chunk 192 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 194 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 overall best weight: 2.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 GLN D 58 GLN E 423 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.061245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.041522 restraints weight = 85228.863| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 3.96 r_work: 0.2603 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20558 Z= 0.226 Angle : 0.578 8.564 28060 Z= 0.306 Chirality : 0.041 0.165 3181 Planarity : 0.003 0.038 3312 Dihedral : 16.632 136.904 3233 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.48 % Allowed : 10.44 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.18), residues: 2248 helix: 1.60 (0.16), residues: 1214 sheet: -0.54 (0.35), residues: 199 loop : -0.90 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 288 TYR 0.018 0.001 TYR A 580 PHE 0.017 0.001 PHE B 376 TRP 0.034 0.002 TRP D 526 HIS 0.006 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00512 (20558) covalent geometry : angle 0.57821 (28060) hydrogen bonds : bond 0.03344 ( 918) hydrogen bonds : angle 4.25867 ( 2642) *********************** 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 104 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 73 time to evaluate : 0.821 Fit side-chains REVERT: A 579 MET cc_start: 0.8401 (tmm) cc_final: 0.7955 (tmm) REVERT: A 602 MET cc_start: 0.8700 (tpp) cc_final: 0.8240 (tpp) REVERT: A 623 MET cc_start: 0.9250 (tpt) cc_final: 0.8759 (tpp) REVERT: B 263 MET cc_start: 0.8495 (mmp) cc_final: 0.8168 (mmm) REVERT: C 71 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8700 (mp10) REVERT: C 306 MET cc_start: 0.9000 (tmm) cc_final: 0.8733 (tmm) REVERT: D 188 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8876 (tt) REVERT: D 497 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8753 (tt) REVERT: D 506 MET cc_start: 0.9030 (tpp) cc_final: 0.8669 (tmm) REVERT: E 140 ASP cc_start: 0.9001 (t70) cc_final: 0.8665 (t0) outliers start: 31 outliers final: 10 residues processed: 98 average time/residue: 0.1141 time to fit residues: 18.8730 Evaluate side-chains 83 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 883 THR 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 188 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain E residue 94 THR 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 100 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 216 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 168 optimal weight: 0.6980 chunk 144 optimal weight: 0.9980 chunk 195 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN B 534 GLN B 538 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.061351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.041484 restraints weight = 84799.559| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 3.97 r_work: 0.2606 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1751 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= 0.191 Angle : 0.547 8.443 28060 Z= 0.290 Chirality : 0.040 0.210 3181 Planarity : 0.003 0.038 3312 Dihedral : 16.631 135.582 3233 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.24 % Allowed : 11.96 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.18), residues: 2248 helix: 1.65 (0.16), residues: 1204 sheet: -0.50 (0.35), residues: 199 loop : -0.88 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 503 TYR 0.017 0.001 TYR A 580 PHE 0.022 0.001 PHE C 392 TRP 0.011 0.001 TRP C 58 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00432 (20558) covalent geometry : angle 0.54719 (28060) hydrogen bonds : bond 0.03175 ( 918) hydrogen bonds : angle 4.18019 ( 2642) *********************** 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 101 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.807 Fit side-chains REVERT: A 560 THR cc_start: 0.8040 (OUTLIER) cc_final: 0.7726 (p) REVERT: A 579 MET cc_start: 0.8390 (tmm) cc_final: 0.8164 (tmm) REVERT: B 263 MET cc_start: 0.8639 (mmp) cc_final: 0.8326 (mmm) REVERT: C 285 LEU cc_start: 0.9744 (tp) cc_final: 0.9451 (tt) REVERT: C 306 MET cc_start: 0.8992 (tmm) cc_final: 0.8642 (tmm) REVERT: C 392 PHE cc_start: 0.8983 (t80) cc_final: 0.8734 (t80) REVERT: C 585 MET cc_start: 0.9264 (tpt) cc_final: 0.9055 (tpt) REVERT: D 188 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8835 (tt) REVERT: D 497 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8706 (tt) REVERT: D 506 MET cc_start: 0.9061 (tpp) cc_final: 0.8816 (tpp) REVERT: E 140 ASP cc_start: 0.9029 (t70) cc_final: 0.8712 (t0) REVERT: E 414 MET cc_start: 0.8353 (tpt) cc_final: 0.8035 (tpt) outliers start: 26 outliers final: 12 residues processed: 98 average time/residue: 0.1326 time to fit residues: 21.5177 Evaluate side-chains 87 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 560 THR Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 497 ILE 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 147 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 223 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 99 optimal weight: 0.1980 chunk 43 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.061114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.041164 restraints weight = 83898.473| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 4.00 r_work: 0.2609 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20558 Z= 0.171 Angle : 0.540 9.001 28060 Z= 0.284 Chirality : 0.040 0.186 3181 Planarity : 0.003 0.038 3312 Dihedral : 16.631 135.170 3233 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.29 % Allowed : 12.87 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.18), residues: 2248 helix: 1.69 (0.16), residues: 1204 sheet: -0.51 (0.35), residues: 197 loop : -0.83 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 398 TYR 0.017 0.001 TYR A 580 PHE 0.017 0.001 PHE B 437 TRP 0.013 0.001 TRP C 58 HIS 0.003 0.001 HIS E 428 Details of bonding type rmsd covalent geometry : bond 0.00390 (20558) covalent geometry : angle 0.54033 (28060) hydrogen bonds : bond 0.03059 ( 918) hydrogen bonds : angle 4.08035 ( 2642) *********************** 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 102 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 0.861 Fit side-chains REVERT: A 485 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7994 (ptpp) REVERT: A 560 THR cc_start: 0.8019 (OUTLIER) cc_final: 0.7703 (p) REVERT: A 579 MET cc_start: 0.8435 (tmm) cc_final: 0.8207 (tmm) REVERT: A 602 MET cc_start: 0.8981 (tpt) cc_final: 0.8679 (tpt) REVERT: B 263 MET cc_start: 0.8674 (mmp) cc_final: 0.8379 (mmm) REVERT: C 285 LEU cc_start: 0.9735 (tp) cc_final: 0.9410 (tt) REVERT: C 306 MET cc_start: 0.8976 (tmm) cc_final: 0.8588 (tmm) REVERT: C 392 PHE cc_start: 0.8832 (t80) cc_final: 0.8625 (t80) REVERT: D 188 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8752 (tt) REVERT: D 497 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8699 (tt) REVERT: D 506 MET cc_start: 0.9090 (tpp) cc_final: 0.8843 (tpp) REVERT: E 140 ASP cc_start: 0.9039 (t70) cc_final: 0.8726 (t0) REVERT: E 414 MET cc_start: 0.8226 (tpt) cc_final: 0.7912 (tpt) outliers start: 27 outliers final: 17 residues processed: 96 average time/residue: 0.1285 time to fit residues: 20.9879 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 : 0.552 ------------------------------------------------------------------------------- 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 574 LYS Chi-restraints excluded: chain A residue 848 THR 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 C residue 199 LEU Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 462 PHE 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 497 ILE 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 178 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 199 optimal weight: 0.2980 chunk 53 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 155 optimal weight: 0.4980 chunk 179 optimal weight: 0.9980 chunk 157 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.061777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.042188 restraints weight = 83425.131| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 3.90 r_work: 0.2668 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20558 Z= 0.119 Angle : 0.517 9.395 28060 Z= 0.273 Chirality : 0.039 0.171 3181 Planarity : 0.003 0.038 3312 Dihedral : 16.569 132.749 3233 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.10 % Allowed : 13.73 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.18), residues: 2248 helix: 1.73 (0.16), residues: 1204 sheet: -0.44 (0.35), residues: 197 loop : -0.81 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 398 TYR 0.017 0.001 TYR C 605 PHE 0.054 0.001 PHE C 334 TRP 0.013 0.001 TRP C 58 HIS 0.003 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00267 (20558) covalent geometry : angle 0.51675 (28060) hydrogen bonds : bond 0.02879 ( 918) hydrogen bonds : angle 3.98714 ( 2642) *********************** 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 98 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.802 Fit side-chains REVERT: A 485 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8165 (ptpp) REVERT: A 523 ASP cc_start: 0.8695 (t0) cc_final: 0.8355 (t0) REVERT: A 579 MET cc_start: 0.8447 (tmm) cc_final: 0.8169 (ppp) REVERT: B 263 MET cc_start: 0.8587 (mmp) cc_final: 0.8320 (mmm) REVERT: C 285 LEU cc_start: 0.9726 (tp) cc_final: 0.9399 (tt) REVERT: C 306 MET cc_start: 0.8965 (tmm) cc_final: 0.8564 (tmm) REVERT: C 392 PHE cc_start: 0.8735 (t80) cc_final: 0.8486 (t80) REVERT: D 188 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8786 (tt) REVERT: D 497 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8774 (tt) REVERT: D 506 MET cc_start: 0.9059 (tpp) cc_final: 0.8838 (tpp) REVERT: E 140 ASP cc_start: 0.9033 (t70) cc_final: 0.8749 (t0) outliers start: 23 outliers final: 12 residues processed: 95 average time/residue: 0.1239 time to fit residues: 20.2078 Evaluate side-chains 87 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 574 LYS Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain C residue 462 PHE 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 497 ILE Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 437 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 192 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 147 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 291 GLN ** 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 = 0.3416 r_free = 0.3416 target = 0.061749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.042383 restraints weight = 83651.061| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 3.85 r_work: 0.2670 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20558 Z= 0.133 Angle : 0.526 11.234 28060 Z= 0.276 Chirality : 0.039 0.184 3181 Planarity : 0.003 0.038 3312 Dihedral : 16.583 132.932 3233 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.00 % Allowed : 13.92 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.18), residues: 2248 helix: 1.78 (0.16), residues: 1197 sheet: -0.40 (0.35), residues: 197 loop : -0.80 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 398 TYR 0.018 0.001 TYR C 605 PHE 0.047 0.001 PHE C 334 TRP 0.013 0.001 TRP C 58 HIS 0.003 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00303 (20558) covalent geometry : angle 0.52590 (28060) hydrogen bonds : bond 0.02909 ( 918) hydrogen bonds : angle 3.98837 ( 2642) *********************** 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 96 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.750 Fit side-chains REVERT: A 485 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8194 (ptpp) REVERT: A 579 MET cc_start: 0.8446 (tmm) cc_final: 0.8199 (ppp) REVERT: C 285 LEU cc_start: 0.9704 (tp) cc_final: 0.9355 (tt) REVERT: C 306 MET cc_start: 0.8946 (tmm) cc_final: 0.8547 (tmm) REVERT: C 361 MET cc_start: 0.9006 (tpp) cc_final: 0.8595 (mmm) REVERT: C 392 PHE cc_start: 0.8685 (t80) cc_final: 0.8438 (t80) REVERT: C 585 MET cc_start: 0.9232 (tpt) cc_final: 0.8990 (tpt) REVERT: D 188 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8783 (tt) REVERT: D 497 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8741 (tt) REVERT: D 506 MET cc_start: 0.9071 (tpp) cc_final: 0.8840 (tpp) REVERT: E 140 ASP cc_start: 0.9045 (t70) cc_final: 0.8753 (t0) outliers start: 21 outliers final: 15 residues processed: 93 average time/residue: 0.1237 time to fit residues: 19.8089 Evaluate side-chains 91 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 574 LYS Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain C residue 462 PHE Chi-restraints excluded: chain D residue 53 GLN 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 497 ILE Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 171 LEU 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 116 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 222 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 224 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 GLN C 97 GLN E 428 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.060179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.040159 restraints weight = 84166.229| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 3.95 r_work: 0.2578 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 20558 Z= 0.250 Angle : 0.604 13.190 28060 Z= 0.315 Chirality : 0.042 0.205 3181 Planarity : 0.003 0.038 3312 Dihedral : 16.841 137.936 3233 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.33 % Allowed : 14.25 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.18), residues: 2248 helix: 1.69 (0.15), residues: 1220 sheet: -0.55 (0.35), residues: 207 loop : -0.81 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 145 TYR 0.021 0.001 TYR A 580 PHE 0.044 0.002 PHE C 334 TRP 0.013 0.001 TRP C 58 HIS 0.004 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00565 (20558) covalent geometry : angle 0.60428 (28060) hydrogen bonds : bond 0.03310 ( 918) hydrogen bonds : angle 4.14123 ( 2642) *********************** 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 99 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 0.716 Fit side-chains REVERT: A 579 MET cc_start: 0.8546 (tmm) cc_final: 0.8116 (tmm) REVERT: A 602 MET cc_start: 0.8568 (tpt) cc_final: 0.7486 (tpt) REVERT: A 623 MET cc_start: 0.8831 (mmm) cc_final: 0.8426 (tpp) REVERT: C 71 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8598 (mt0) REVERT: C 285 LEU cc_start: 0.9726 (tp) cc_final: 0.9389 (tt) REVERT: C 306 MET cc_start: 0.8967 (tmm) cc_final: 0.8585 (tmm) REVERT: C 361 MET cc_start: 0.8970 (tpp) cc_final: 0.8579 (mmm) REVERT: C 392 PHE cc_start: 0.8754 (t80) cc_final: 0.8512 (t80) REVERT: C 517 MET cc_start: 0.9243 (tmm) cc_final: 0.9030 (ppp) REVERT: C 585 MET cc_start: 0.9260 (tpt) cc_final: 0.8986 (tpt) REVERT: D 188 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8643 (tt) REVERT: D 506 MET cc_start: 0.9029 (tpp) cc_final: 0.8737 (tpp) REVERT: E 140 ASP cc_start: 0.9040 (t70) cc_final: 0.8710 (t0) outliers start: 28 outliers final: 19 residues processed: 96 average time/residue: 0.1284 time to fit residues: 20.9613 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 : 0.792 ------------------------------------------------------------------------------- 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 829 ILE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 462 PHE Chi-restraints excluded: chain D residue 53 GLN 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 497 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 437 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 43 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 chunk 175 optimal weight: 3.9990 chunk 129 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 205 optimal weight: 0.7980 chunk 189 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.060792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.040842 restraints weight = 83881.406| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 3.97 r_work: 0.2600 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20558 Z= 0.163 Angle : 0.558 14.454 28060 Z= 0.290 Chirality : 0.040 0.233 3181 Planarity : 0.003 0.038 3312 Dihedral : 16.746 135.338 3233 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.91 % Allowed : 14.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.18), residues: 2248 helix: 1.75 (0.15), residues: 1216 sheet: -0.44 (0.36), residues: 198 loop : -0.79 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 398 TYR 0.017 0.001 TYR A 580 PHE 0.040 0.001 PHE C 334 TRP 0.013 0.001 TRP C 58 HIS 0.003 0.001 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00371 (20558) covalent geometry : angle 0.55766 (28060) hydrogen bonds : bond 0.03049 ( 918) hydrogen bonds : angle 4.03899 ( 2642) ********************** 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 92 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.613 Fit side-chains REVERT: A 579 MET cc_start: 0.8496 (tmm) cc_final: 0.8221 (tmm) REVERT: A 602 MET cc_start: 0.8537 (tpt) cc_final: 0.7360 (tpt) REVERT: A 623 MET cc_start: 0.8818 (mmm) cc_final: 0.8394 (tpp) REVERT: A 792 THR cc_start: 0.9574 (OUTLIER) cc_final: 0.9320 (p) REVERT: C 285 LEU cc_start: 0.9721 (tp) cc_final: 0.9386 (tt) REVERT: C 306 MET cc_start: 0.8968 (tmm) cc_final: 0.8586 (tmm) REVERT: C 361 MET cc_start: 0.8959 (tpp) cc_final: 0.8567 (mmm) REVERT: C 392 PHE cc_start: 0.8748 (t80) cc_final: 0.8448 (t80) REVERT: C 517 MET cc_start: 0.9179 (tmm) cc_final: 0.8933 (ppp) REVERT: C 585 MET cc_start: 0.9210 (tpt) cc_final: 0.8955 (tpt) REVERT: D 188 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8635 (tt) REVERT: D 497 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8629 (tt) REVERT: D 506 MET cc_start: 0.9033 (tpp) cc_final: 0.8737 (tpp) REVERT: E 140 ASP cc_start: 0.9041 (t70) cc_final: 0.8714 (t0) outliers start: 19 outliers final: 16 residues processed: 89 average time/residue: 0.1241 time to fit residues: 18.9280 Evaluate side-chains 91 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 574 LYS Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 462 PHE Chi-restraints excluded: chain D residue 53 GLN 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 497 ILE 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 Chi-restraints excluded: chain E residue 437 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 48 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 137 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 428 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.060779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.040761 restraints weight = 84975.102| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 4.01 r_work: 0.2597 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20558 Z= 0.178 Angle : 0.555 13.551 28060 Z= 0.290 Chirality : 0.040 0.209 3181 Planarity : 0.003 0.038 3312 Dihedral : 16.768 135.708 3233 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.95 % Allowed : 14.82 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.18), residues: 2248 helix: 1.75 (0.15), residues: 1222 sheet: -0.46 (0.37), residues: 188 loop : -0.73 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 398 TYR 0.017 0.001 TYR A 580 PHE 0.059 0.001 PHE C 334 TRP 0.014 0.001 TRP C 58 HIS 0.003 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00406 (20558) covalent geometry : angle 0.55490 (28060) hydrogen bonds : bond 0.03019 ( 918) hydrogen bonds : angle 4.02571 ( 2642) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4403.20 seconds wall clock time: 76 minutes 24.23 seconds (4584.23 seconds total)