Starting phenix.real_space_refine on Thu Jul 2 16:30:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9huh_52413/07_2026/9huh_52413.cif Found real_map, /net/cci-nas-00/data/ceres_data/9huh_52413/07_2026/9huh_52413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9huh_52413/07_2026/9huh_52413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9huh_52413/07_2026/9huh_52413.map" model { file = "/net/cci-nas-00/data/ceres_data/9huh_52413/07_2026/9huh_52413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9huh_52413/07_2026/9huh_52413.cif" } resolution = 2.96 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= 0.001 sd= 0.017 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: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 60 5.16 5 C 5723 2.51 5 N 1488 2.21 5 O 1675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8952 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4462 Classifications: {'peptide': 571} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 41, 'TRANS': 529} Chain breaks: 9 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4477 Classifications: {'peptide': 573} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 42, 'TRANS': 530} Chain breaks: 9 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 2.11, per 1000 atoms: 0.24 Number of scatterers: 8952 At special positions: 0 Unit cell: (141.215, 92.1704, 71.0304, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 60 16.00 O 1675 8.00 N 1488 7.00 C 5723 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: 0.69 Conformation dependent library (CDL) restraints added in 429.5 milliseconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 25 sheets defined 21.2% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 173 through 180 removed outlier: 3.777A pdb=" N GLN A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET A 180 " --> pdb=" O ASP A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 196 removed outlier: 3.817A pdb=" N ASN A 196 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 209 removed outlier: 4.146A pdb=" N ASP A 209 " --> pdb=" O SER A 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 206 through 209' Processing helix chain 'A' and resid 316 through 330 Processing helix chain 'A' and resid 402 through 408 removed outlier: 6.350A pdb=" N PHE A 407 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLY A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 454 removed outlier: 3.581A pdb=" N GLN A 454 " --> pdb=" O PHE A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 474 Processing helix chain 'A' and resid 494 through 507 removed outlier: 3.686A pdb=" N TYR A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A 499 " --> pdb=" O ARG A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 531 Processing helix chain 'A' and resid 534 through 557 removed outlier: 3.591A pdb=" N SER A 540 " --> pdb=" O ARG A 536 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 542 " --> pdb=" O HIS A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 562 No H-bonds generated for 'chain 'A' and resid 560 through 562' Processing helix chain 'A' and resid 575 through 577 No H-bonds generated for 'chain 'A' and resid 575 through 577' Processing helix chain 'A' and resid 611 through 620 Processing helix chain 'A' and resid 621 through 624 Processing helix chain 'A' and resid 657 through 661 Processing helix chain 'B' and resid 173 through 178 Processing helix chain 'B' and resid 192 through 195 Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 315 through 330 removed outlier: 3.853A pdb=" N PHE B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER B 322 " --> pdb=" O ASP B 318 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 408 removed outlier: 3.903A pdb=" N ASP B 405 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER B 406 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N PHE B 407 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 402 through 408' Processing helix chain 'B' and resid 444 through 454 removed outlier: 3.562A pdb=" N GLN B 454 " --> pdb=" O PHE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 474 Processing helix chain 'B' and resid 494 through 506 removed outlier: 3.738A pdb=" N TYR B 498 " --> pdb=" O PRO B 494 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 499 " --> pdb=" O ARG B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 531 Processing helix chain 'B' and resid 532 through 554 removed outlier: 3.850A pdb=" N GLU B 537 " --> pdb=" O LYS B 533 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP B 548 " --> pdb=" O ARG B 544 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN B 549 " --> pdb=" O CYS B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 562 No H-bonds generated for 'chain 'B' and resid 560 through 562' Processing helix chain 'B' and resid 575 through 577 No H-bonds generated for 'chain 'B' and resid 575 through 577' Processing helix chain 'B' and resid 610 through 621 Processing helix chain 'B' and resid 622 through 624 No H-bonds generated for 'chain 'B' and resid 622 through 624' Processing helix chain 'B' and resid 657 through 661 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 8 removed outlier: 7.068A pdb=" N ILE A 7 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL A 76 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 16 removed outlier: 6.979A pdb=" N THR A 15 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN A 90 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 19 through 20 removed outlier: 6.291A pdb=" N CYS A 19 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ILE A 115 " --> pdb=" O CYS A 19 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASP A 248 " --> pdb=" O ALA A 216 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 39 through 40 removed outlier: 3.590A pdb=" N TRP A 68 " --> pdb=" O PHE A 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 148 through 150 removed outlier: 3.859A pdb=" N ALA A 148 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU A 271 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLN A 286 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE A 269 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N SER A 288 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU A 267 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL A 290 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE A 265 " --> pdb=" O VAL A 290 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 333 through 334 removed outlier: 3.921A pdb=" N LYS A 333 " --> pdb=" O GLN A 306 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG A 650 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 356 Processing sheet with id=AA8, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA9, first strand: chain 'A' and resid 416 through 418 Processing sheet with id=AB1, first strand: chain 'A' and resid 476 through 480 removed outlier: 3.532A pdb=" N ARG A 488 " --> pdb=" O VAL A 479 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ILE A 565 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LEU A 489 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE A 567 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU A 491 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 571 through 574 Processing sheet with id=AB3, first strand: chain 'A' and resid 590 through 591 removed outlier: 6.138A pdb=" N LEU A 596 " --> pdb=" O THR A 628 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE A 630 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE A 598 " --> pdb=" O ILE A 630 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 605 through 606 Processing sheet with id=AB5, first strand: chain 'B' and resid 6 through 8 removed outlier: 6.798A pdb=" N ILE B 7 " --> pdb=" O ASP B 28 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL B 76 " --> pdb=" O LEU B 27 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 15 through 16 removed outlier: 3.582A pdb=" N ALA B 106 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN B 93 " --> pdb=" O ASN B 43 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 19 through 20 removed outlier: 6.524A pdb=" N CYS B 19 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ILE B 115 " --> pdb=" O CYS B 19 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR B 187 " --> pdb=" O HIS B 245 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS B 245 " --> pdb=" O THR B 187 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 148 through 150 removed outlier: 3.724A pdb=" N ALA B 148 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU B 271 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLN B 286 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE B 269 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER B 288 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU B 267 " --> pdb=" O SER B 288 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL B 290 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE B 265 " --> pdb=" O VAL B 290 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 333 through 334 removed outlier: 4.057A pdb=" N LYS B 333 " --> pdb=" O GLN B 306 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG B 650 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 352 through 356 removed outlier: 4.306A pdb=" N ASP B 369 " --> pdb=" O VAL B 392 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 410 through 412 removed outlier: 6.692A pdb=" N ILE B 428 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU B 462 " --> pdb=" O ILE B 428 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N PHE B 430 " --> pdb=" O LEU B 462 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 416 through 418 Processing sheet with id=AC4, first strand: chain 'B' and resid 476 through 480 removed outlier: 8.038A pdb=" N ILE B 565 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU B 489 " --> pdb=" O ILE B 565 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ILE B 567 " --> pdb=" O LEU B 489 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU B 491 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 513 through 514 Processing sheet with id=AC6, first strand: chain 'B' and resid 571 through 573 Processing sheet with id=AC7, first strand: chain 'B' and resid 596 through 599 removed outlier: 6.564A pdb=" N LEU B 596 " --> pdb=" O THR B 628 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ILE B 630 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE B 598 " --> pdb=" O ILE B 630 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 257 hydrogen bonds defined for protein. 669 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.60 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1488 1.31 - 1.44: 2324 1.44 - 1.56: 5242 1.56 - 1.69: 5 1.69 - 1.81: 87 Bond restraints: 9146 Sorted by residual: bond pdb=" C LYS B 100 " pdb=" O LYS B 100 " ideal model delta sigma weight residual 1.236 1.438 -0.202 1.31e-02 5.83e+03 2.37e+02 bond pdb=" CA HIS B 595 " pdb=" C HIS B 595 " ideal model delta sigma weight residual 1.520 1.642 -0.122 1.20e-02 6.94e+03 1.03e+02 bond pdb=" CA HIS B 595 " pdb=" CB HIS B 595 " ideal model delta sigma weight residual 1.534 1.697 -0.164 1.72e-02 3.38e+03 9.07e+01 bond pdb=" N LEU B 596 " pdb=" CA LEU B 596 " ideal model delta sigma weight residual 1.457 1.594 -0.137 1.53e-02 4.27e+03 8.03e+01 bond pdb=" C HIS B 595 " pdb=" N LEU B 596 " ideal model delta sigma weight residual 1.330 1.434 -0.103 1.19e-02 7.06e+03 7.51e+01 ... (remaining 9141 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.92: 12387 6.92 - 13.84: 22 13.84 - 20.76: 4 20.76 - 27.69: 0 27.69 - 34.61: 1 Bond angle restraints: 12414 Sorted by residual: angle pdb=" C HIS B 595 " pdb=" CA HIS B 595 " pdb=" CB HIS B 595 " ideal model delta sigma weight residual 109.65 144.26 -34.61 1.75e+00 3.27e-01 3.91e+02 angle pdb=" N LEU B 596 " pdb=" CA LEU B 596 " pdb=" C LEU B 596 " ideal model delta sigma weight residual 108.34 127.65 -19.31 1.31e+00 5.83e-01 2.17e+02 angle pdb=" C VAL A 227 " pdb=" CA VAL A 227 " pdb=" CB VAL A 227 " ideal model delta sigma weight residual 111.08 96.32 14.76 1.17e+00 7.31e-01 1.59e+02 angle pdb=" CA HIS B 595 " pdb=" C HIS B 595 " pdb=" N LEU B 596 " ideal model delta sigma weight residual 116.31 129.47 -13.16 1.48e+00 4.57e-01 7.90e+01 angle pdb=" C LEU A 623 " pdb=" CA LEU A 623 " pdb=" CB LEU A 623 " ideal model delta sigma weight residual 110.37 95.15 15.22 1.78e+00 3.16e-01 7.31e+01 ... (remaining 12409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 4886 17.75 - 35.51: 454 35.51 - 53.26: 135 53.26 - 71.01: 26 71.01 - 88.77: 9 Dihedral angle restraints: 5510 sinusoidal: 2220 harmonic: 3290 Sorted by residual: dihedral pdb=" C HIS B 595 " pdb=" N HIS B 595 " pdb=" CA HIS B 595 " pdb=" CB HIS B 595 " ideal model delta harmonic sigma weight residual -122.60 -148.91 26.31 0 2.50e+00 1.60e-01 1.11e+02 dihedral pdb=" C LEU A 623 " pdb=" N LEU A 623 " pdb=" CA LEU A 623 " pdb=" CB LEU A 623 " ideal model delta harmonic sigma weight residual -122.60 -104.55 -18.05 0 2.50e+00 1.60e-01 5.21e+01 dihedral pdb=" C GLU B 474 " pdb=" N GLU B 474 " pdb=" CA GLU B 474 " pdb=" CB GLU B 474 " ideal model delta harmonic sigma weight residual -122.60 -140.39 17.79 0 2.50e+00 1.60e-01 5.06e+01 ... (remaining 5507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1207 0.105 - 0.210: 185 0.210 - 0.315: 12 0.315 - 0.419: 3 0.419 - 0.524: 2 Chirality restraints: 1409 Sorted by residual: chirality pdb=" CA GLU B 474 " pdb=" N GLU B 474 " pdb=" C GLU B 474 " pdb=" CB GLU B 474 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.87e+00 chirality pdb=" CA ILE B 313 " pdb=" N ILE B 313 " pdb=" C ILE B 313 " pdb=" CB ILE B 313 " both_signs ideal model delta sigma weight residual False 2.43 2.87 -0.44 2.00e-01 2.50e+01 4.79e+00 chirality pdb=" CA HIS B 595 " pdb=" N HIS B 595 " pdb=" C HIS B 595 " pdb=" CB HIS B 595 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.27e+00 ... (remaining 1406 not shown) Planarity restraints: 1592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 480 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C PRO A 480 " -0.056 2.00e-02 2.50e+03 pdb=" O PRO A 480 " 0.021 2.00e-02 2.50e+03 pdb=" N ALA A 481 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 503 " -0.014 2.00e-02 2.50e+03 2.72e-02 7.40e+00 pdb=" C GLU A 503 " 0.047 2.00e-02 2.50e+03 pdb=" O GLU A 503 " -0.018 2.00e-02 2.50e+03 pdb=" N GLN A 504 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 228 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.13e+00 pdb=" C VAL A 228 " -0.035 2.00e-02 2.50e+03 pdb=" O VAL A 228 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU A 229 " 0.012 2.00e-02 2.50e+03 ... (remaining 1589 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 15 2.30 - 2.95: 4116 2.95 - 3.60: 11703 3.60 - 4.25: 20087 4.25 - 4.90: 33331 Nonbonded interactions: 69252 Sorted by model distance: nonbonded pdb=" OD2 ASP B 157 " pdb="CA CA B 702 " model vdw 1.649 3.250 nonbonded pdb=" OD2 ASP B 483 " pdb=" NH2 ARG B 488 " model vdw 1.683 3.120 nonbonded pdb=" OD2 ASP A 155 " pdb=" CD2 LEU A 364 " model vdw 1.964 3.460 nonbonded pdb=" CG2 THR B 111 " pdb=" O HOH B 803 " model vdw 2.203 3.460 nonbonded pdb=" OH TYR A 435 " pdb=" OH TYR B 237 " model vdw 2.217 3.040 ... (remaining 69247 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 2 through 314 or (resid 315 and (name N or name CA or name \ C or name O or name CB )) or resid 316 through 370 or resid 388 through 703)) } 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: 4.410 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.620 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:6.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2132 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 : 0.010 0.202 9146 Z= 0.671 Angle : 1.351 34.607 12414 Z= 0.915 Chirality : 0.075 0.524 1409 Planarity : 0.006 0.065 1592 Dihedral : 15.447 88.766 3368 Min Nonbonded Distance : 1.649 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.16 % Favored : 93.39 % Rotamer: Outliers : 3.36 % Allowed : 22.83 % Favored : 73.81 % Cbeta Deviations : 0.47 % 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 are not related in a simple way. whole: -2.79 (0.23), residues: 1104 helix: -0.89 (0.39), residues: 177 sheet: -1.23 (0.28), residues: 336 loop : -2.60 (0.21), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 419 TYR 0.032 0.002 TYR A 356 PHE 0.019 0.002 PHE A 478 TRP 0.033 0.003 TRP B 141 HIS 0.009 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00981 / 0.67 ( 9146) covalent geometry : angle 1.35073 / 0.91 (12414) hydrogen bonds : bond 0.20931 / 14.37 ( 257) hydrogen bonds : angle 7.84715 / 5.45 ( 669) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 85 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 LEU cc_start: 0.0916 (OUTLIER) cc_final: -0.0492 (mp) REVERT: B 21 LEU cc_start: 0.3330 (OUTLIER) cc_final: 0.2811 (pp) REVERT: B 269 ILE cc_start: 0.1860 (tp) cc_final: 0.1382 (tp) REVERT: B 479 VAL cc_start: -0.0323 (OUTLIER) cc_final: -0.1969 (t) outliers start: 34 outliers final: 3 residues processed: 115 average time/residue: 0.4126 time to fit residues: 52.0750 Evaluate side-chains 78 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 479 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.2980 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 GLN A 93 GLN ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 HIS A 276 ASN A 358 GLN A 444 HIS A 448 GLN A 505 GLN A 509 HIS ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN B 136 GLN B 202 HIS ** B 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 GLN B 504 GLN ** B 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.181922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.166408 restraints weight = 12803.557| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 2.37 r_work: 0.4011 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4289 moved from start: 0.6022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 9146 Z= 0.254 Angle : 0.940 13.734 12414 Z= 0.481 Chirality : 0.056 0.256 1409 Planarity : 0.008 0.063 1592 Dihedral : 6.305 41.596 1198 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 5.73 % Allowed : 20.45 % Favored : 73.81 % 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 are not related in a simple way. whole: -2.26 (0.23), residues: 1104 helix: -0.88 (0.37), residues: 182 sheet: -0.73 (0.28), residues: 338 loop : -2.22 (0.22), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 212 TYR 0.027 0.003 TYR A 250 PHE 0.023 0.003 PHE B 475 TRP 0.025 0.004 TRP A 141 HIS 0.019 0.003 HIS B 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.25 ( 9146) covalent geometry : angle 0.94013 / 0.48 (12414) hydrogen bonds : bond 0.05243 / 3.57 ( 257) hydrogen bonds : angle 6.25376 / 4.47 ( 669) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 117 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 PHE cc_start: 0.5933 (OUTLIER) cc_final: 0.5520 (t80) REVERT: A 432 ASP cc_start: 0.6864 (OUTLIER) cc_final: 0.6629 (p0) REVERT: A 538 HIS cc_start: 0.7671 (m170) cc_final: 0.7384 (m170) REVERT: B 67 THR cc_start: 0.6796 (p) cc_final: 0.6408 (p) outliers start: 58 outliers final: 20 residues processed: 158 average time/residue: 0.3985 time to fit residues: 69.1455 Evaluate side-chains 125 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 358 GLN Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 454 GLN Chi-restraints excluded: chain B residue 630 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 0.3980 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 51 optimal weight: 0.0570 chunk 43 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 ASN A 136 GLN A 276 ASN A 361 HIS A 448 GLN ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 HIS B 215 GLN B 358 GLN B 442 GLN B 455 GLN B 471 HIS B 539 ASN B 595 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.185843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.170078 restraints weight = 12911.718| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 2.42 r_work: 0.4017 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 1.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 9146 Z= 0.331 Angle : 1.036 19.203 12414 Z= 0.533 Chirality : 0.057 0.493 1409 Planarity : 0.008 0.063 1592 Dihedral : 6.508 53.513 1191 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 7.41 % Allowed : 20.85 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -2.31 (0.23), residues: 1104 helix: -0.61 (0.38), residues: 174 sheet: -1.01 (0.28), residues: 322 loop : -2.16 (0.22), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 550 TYR 0.033 0.003 TYR B 109 PHE 0.034 0.003 PHE B 475 TRP 0.043 0.004 TRP B 233 HIS 0.013 0.003 HIS B 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.33 ( 9146) covalent geometry : angle 1.03580 / 0.53 (12414) hydrogen bonds : bond 0.07080 / 4.75 ( 257) hydrogen bonds : angle 6.53493 / 4.67 ( 669) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 224 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.6906 (OUTLIER) cc_final: 0.6414 (mtmt) REVERT: A 211 VAL cc_start: 0.5017 (OUTLIER) cc_final: 0.4688 (p) REVERT: A 244 LYS cc_start: 0.6401 (OUTLIER) cc_final: 0.5827 (mttp) REVERT: A 461 LYS cc_start: 0.7737 (mtpt) cc_final: 0.7345 (mtpt) REVERT: A 488 ARG cc_start: 0.7579 (mpt90) cc_final: 0.7373 (mpt180) REVERT: A 657 LYS cc_start: 0.7826 (mmmt) cc_final: 0.7511 (mppt) REVERT: B 113 VAL cc_start: 0.7606 (p) cc_final: 0.7369 (t) REVERT: B 266 THR cc_start: 0.7973 (t) cc_final: 0.7747 (m) REVERT: B 411 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6821 (mm-30) REVERT: B 504 GLN cc_start: 0.5292 (OUTLIER) cc_final: 0.4832 (tm-30) REVERT: B 539 ASN cc_start: 0.7838 (OUTLIER) cc_final: 0.6978 (m110) REVERT: B 547 ASP cc_start: 0.7361 (m-30) cc_final: 0.7082 (m-30) REVERT: B 569 GLN cc_start: 0.7363 (mm-40) cc_final: 0.6978 (tp-100) outliers start: 75 outliers final: 14 residues processed: 274 average time/residue: 0.4709 time to fit residues: 139.4900 Evaluate side-chains 214 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 195 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 539 ASN Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 609 ARG Chi-restraints excluded: chain B residue 630 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 18 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 100 optimal weight: 0.4980 chunk 53 optimal weight: 0.0870 chunk 91 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 67 optimal weight: 0.1980 chunk 85 optimal weight: 0.9980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 245 HIS B 358 GLN ** B 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.169311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.151809 restraints weight = 12587.783| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.53 r_work: 0.3831 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 1.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9146 Z= 0.167 Angle : 0.713 11.400 12414 Z= 0.356 Chirality : 0.047 0.156 1409 Planarity : 0.007 0.058 1592 Dihedral : 5.305 53.067 1191 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.55 % Allowed : 25.79 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.24), residues: 1104 helix: -0.40 (0.37), residues: 194 sheet: -0.54 (0.28), residues: 333 loop : -2.04 (0.23), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 205 TYR 0.018 0.002 TYR B 96 PHE 0.022 0.002 PHE A 194 TRP 0.030 0.003 TRP B 233 HIS 0.007 0.001 HIS B 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 9146) covalent geometry : angle 0.71328 / 0.36 (12414) hydrogen bonds : bond 0.04299 / 2.93 ( 257) hydrogen bonds : angle 5.24997 / 3.62 ( 669) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 228 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 TYR cc_start: 0.7362 (m-80) cc_final: 0.7117 (m-80) REVERT: A 105 LYS cc_start: 0.7163 (mtmm) cc_final: 0.6908 (mtmm) REVERT: A 200 VAL cc_start: 0.7720 (OUTLIER) cc_final: 0.7400 (t) REVERT: A 461 LYS cc_start: 0.7831 (mtpt) cc_final: 0.7551 (mtpt) REVERT: A 505 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7197 (tt0) REVERT: A 547 ASP cc_start: 0.7798 (m-30) cc_final: 0.7360 (m-30) REVERT: A 566 ASP cc_start: 0.6762 (m-30) cc_final: 0.6554 (m-30) REVERT: A 596 LEU cc_start: 0.8050 (mt) cc_final: 0.7842 (mp) REVERT: A 618 SER cc_start: 0.8077 (t) cc_final: 0.7547 (p) REVERT: A 657 LYS cc_start: 0.7782 (mmmt) cc_final: 0.7511 (mppt) REVERT: B 97 TYR cc_start: 0.4769 (OUTLIER) cc_final: 0.3981 (p90) REVERT: B 180 MET cc_start: 0.6330 (OUTLIER) cc_final: 0.6028 (mmm) REVERT: B 212 ARG cc_start: 0.7890 (ptp90) cc_final: 0.7604 (ptp-170) REVERT: B 233 TRP cc_start: 0.7820 (m-90) cc_final: 0.7600 (m-90) REVERT: B 244 LYS cc_start: 0.7404 (mtpp) cc_final: 0.6749 (tttp) REVERT: B 432 ASP cc_start: 0.7962 (p0) cc_final: 0.7240 (p0) REVERT: B 477 SER cc_start: 0.8246 (p) cc_final: 0.8000 (p) REVERT: B 495 ARG cc_start: 0.7565 (ttm110) cc_final: 0.7244 (ttm110) REVERT: B 502 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7347 (tp-100) REVERT: B 561 GLU cc_start: 0.7719 (tp30) cc_final: 0.7485 (tp30) outliers start: 46 outliers final: 12 residues processed: 255 average time/residue: 0.5110 time to fit residues: 139.8893 Evaluate side-chains 223 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 206 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 505 GLN Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 502 GLN Chi-restraints excluded: chain B residue 582 PHE Chi-restraints excluded: chain B residue 609 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 109 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 55 optimal weight: 0.0170 chunk 36 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 7 optimal weight: 0.0470 chunk 113 optimal weight: 0.9980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 509 HIS A 595 HIS A 607 ASN B 90 GLN B 196 ASN B 202 HIS B 245 HIS B 358 GLN B 442 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.162485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.144758 restraints weight = 12269.074| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.53 r_work: 0.3737 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 1.7043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9146 Z= 0.167 Angle : 0.727 13.374 12414 Z= 0.369 Chirality : 0.046 0.150 1409 Planarity : 0.007 0.056 1592 Dihedral : 5.158 50.895 1191 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.24 % Allowed : 27.27 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -1.50 (0.24), residues: 1104 helix: 0.13 (0.38), residues: 181 sheet: -0.23 (0.29), residues: 326 loop : -1.84 (0.23), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 205 TYR 0.018 0.002 TYR B 96 PHE 0.019 0.002 PHE B 368 TRP 0.021 0.002 TRP B 233 HIS 0.005 0.001 HIS A 509 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 9146) covalent geometry : angle 0.72710 / 0.37 (12414) hydrogen bonds : bond 0.04763 / 3.28 ( 257) hydrogen bonds : angle 5.20202 / 3.56 ( 669) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 214 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PRO cc_start: 0.7888 (Cg_endo) cc_final: 0.7603 (Cg_exo) REVERT: A 186 SER cc_start: 0.8050 (m) cc_final: 0.7774 (t) REVERT: A 189 THR cc_start: 0.7783 (t) cc_final: 0.7561 (p) REVERT: A 244 LYS cc_start: 0.6988 (ptpp) cc_final: 0.6640 (mttp) REVERT: A 410 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7622 (mp) REVERT: A 411 GLU cc_start: 0.7107 (mm-30) cc_final: 0.6866 (mm-30) REVERT: A 505 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7356 (tt0) REVERT: A 525 LYS cc_start: 0.8016 (mtmt) cc_final: 0.7666 (mtmm) REVERT: A 589 MET cc_start: 0.6327 (pp-130) cc_final: 0.6008 (pp-130) REVERT: B 244 LYS cc_start: 0.7273 (mtpp) cc_final: 0.6709 (tttp) REVERT: B 281 GLU cc_start: 0.7271 (pm20) cc_final: 0.6995 (pm20) REVERT: B 358 GLN cc_start: 0.7526 (tt0) cc_final: 0.7284 (tt0) REVERT: B 574 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7802 (tppp) outliers start: 53 outliers final: 18 residues processed: 245 average time/residue: 0.5407 time to fit residues: 141.6889 Evaluate side-chains 226 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 505 GLN Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 580 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 69 optimal weight: 0.0980 chunk 24 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 48 optimal weight: 0.3980 chunk 98 optimal weight: 0.4980 chunk 71 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 3 GLN B 90 GLN B 136 GLN B 358 GLN B 442 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.158885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.141130 restraints weight = 12275.946| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.51 r_work: 0.3693 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 1.7764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9146 Z= 0.160 Angle : 0.696 11.729 12414 Z= 0.347 Chirality : 0.046 0.167 1409 Planarity : 0.006 0.050 1592 Dihedral : 5.027 52.419 1191 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.05 % Allowed : 27.77 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -1.20 (0.24), residues: 1104 helix: 0.50 (0.39), residues: 181 sheet: -0.15 (0.28), residues: 344 loop : -1.67 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 484 TYR 0.018 0.001 TYR B 96 PHE 0.013 0.002 PHE B 475 TRP 0.020 0.002 TRP A 233 HIS 0.004 0.001 HIS A 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 ( 9146) covalent geometry : angle 0.69627 / 0.35 (12414) hydrogen bonds : bond 0.04264 / 2.90 ( 257) hydrogen bonds : angle 5.00267 / 3.41 ( 669) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 209 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 SER cc_start: 0.8186 (m) cc_final: 0.7792 (t) REVERT: A 244 LYS cc_start: 0.7173 (ptpp) cc_final: 0.6810 (mttp) REVERT: A 328 MET cc_start: 0.5609 (OUTLIER) cc_final: 0.4846 (mmt) REVERT: A 352 MET cc_start: 0.6177 (tmm) cc_final: 0.5949 (tmm) REVERT: A 441 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7576 (ptt180) REVERT: A 505 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.7544 (tt0) REVERT: A 525 LYS cc_start: 0.7894 (mtmt) cc_final: 0.7465 (mtmm) REVERT: A 547 ASP cc_start: 0.7862 (m-30) cc_final: 0.7568 (m-30) REVERT: A 589 MET cc_start: 0.6419 (pp-130) cc_final: 0.6118 (pmm) REVERT: A 596 LEU cc_start: 0.8067 (mt) cc_final: 0.7853 (mp) REVERT: B 107 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7946 (mt) REVERT: B 232 LYS cc_start: 0.7024 (ptpp) cc_final: 0.6796 (ptpp) REVERT: B 244 LYS cc_start: 0.7256 (mtpp) cc_final: 0.6737 (tttp) REVERT: B 281 GLU cc_start: 0.7365 (pm20) cc_final: 0.7144 (pm20) REVERT: B 358 GLN cc_start: 0.7622 (tt0) cc_final: 0.7329 (tt0) REVERT: B 528 ASN cc_start: 0.8223 (m-40) cc_final: 0.7953 (m110) REVERT: B 574 LYS cc_start: 0.8031 (mmtm) cc_final: 0.7771 (tppp) REVERT: B 621 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7304 (mp0) outliers start: 41 outliers final: 16 residues processed: 231 average time/residue: 0.5474 time to fit residues: 135.3768 Evaluate side-chains 222 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 441 ARG Chi-restraints excluded: chain A residue 505 GLN Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 595 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 58 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 113 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 HIS A 504 GLN A 509 HIS B 3 GLN B 196 ASN B 442 GLN B 448 GLN B 505 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.153233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.135369 restraints weight = 12062.955| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.47 r_work: 0.3634 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 1.8646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 9146 Z= 0.232 Angle : 0.776 13.539 12414 Z= 0.391 Chirality : 0.050 0.200 1409 Planarity : 0.007 0.060 1592 Dihedral : 5.377 43.156 1191 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.85 % Allowed : 28.75 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -1.21 (0.24), residues: 1104 helix: 0.44 (0.39), residues: 180 sheet: -0.17 (0.28), residues: 344 loop : -1.64 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 484 TYR 0.029 0.002 TYR B 109 PHE 0.015 0.002 PHE B 194 TRP 0.031 0.004 TRP A 233 HIS 0.015 0.002 HIS A 509 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.23 ( 9146) covalent geometry : angle 0.77615 / 0.39 (12414) hydrogen bonds : bond 0.05300 / 3.63 ( 257) hydrogen bonds : angle 5.49271 / 3.74 ( 669) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 219 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 THR cc_start: 0.7823 (p) cc_final: 0.7429 (t) REVERT: A 186 SER cc_start: 0.8284 (m) cc_final: 0.7754 (t) REVERT: A 244 LYS cc_start: 0.7380 (ptpp) cc_final: 0.7024 (mttp) REVERT: A 411 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7071 (mm-30) REVERT: A 441 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7681 (ptt180) REVERT: A 505 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8289 (tm-30) REVERT: A 525 LYS cc_start: 0.8090 (mtmt) cc_final: 0.7660 (mtmm) REVERT: A 618 SER cc_start: 0.8021 (t) cc_final: 0.7533 (p) REVERT: B 21 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7412 (mt) REVERT: B 180 MET cc_start: 0.6907 (OUTLIER) cc_final: 0.6608 (mmt) REVERT: B 244 LYS cc_start: 0.7287 (mtpp) cc_final: 0.6714 (tttp) REVERT: B 281 GLU cc_start: 0.7487 (pm20) cc_final: 0.7198 (pt0) REVERT: B 502 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7789 (mm110) REVERT: B 580 GLU cc_start: 0.7624 (pt0) cc_final: 0.7314 (pt0) REVERT: B 631 ASN cc_start: 0.7154 (p0) cc_final: 0.6890 (p0) outliers start: 39 outliers final: 20 residues processed: 235 average time/residue: 0.5921 time to fit residues: 148.1457 Evaluate side-chains 236 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 211 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 441 ARG Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 505 GLN Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 419 ARG Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 502 GLN Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 595 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 56 optimal weight: 0.5980 chunk 15 optimal weight: 0.1980 chunk 63 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 72 optimal weight: 0.1980 chunk 96 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 84 optimal weight: 0.0770 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 GLN A 444 HIS B 442 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.155553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.138253 restraints weight = 12057.047| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.45 r_work: 0.3670 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 1.8776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9146 Z= 0.141 Angle : 0.690 10.791 12414 Z= 0.345 Chirality : 0.046 0.180 1409 Planarity : 0.007 0.057 1592 Dihedral : 4.997 42.493 1191 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.06 % Allowed : 29.94 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -0.86 (0.25), residues: 1104 helix: 0.68 (0.40), residues: 178 sheet: 0.08 (0.28), residues: 343 loop : -1.40 (0.24), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 484 TYR 0.015 0.001 TYR B 96 PHE 0.025 0.002 PHE A 515 TRP 0.028 0.002 TRP B 233 HIS 0.003 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 9146) covalent geometry : angle 0.69030 / 0.35 (12414) hydrogen bonds : bond 0.04301 / 2.92 ( 257) hydrogen bonds : angle 5.12103 / 3.48 ( 669) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 SER cc_start: 0.8215 (m) cc_final: 0.7666 (t) REVERT: A 500 LEU cc_start: 0.7484 (mt) cc_final: 0.7187 (tt) REVERT: A 505 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8355 (tm-30) REVERT: A 525 LYS cc_start: 0.7993 (mtmt) cc_final: 0.7578 (mtmm) REVERT: A 589 MET cc_start: 0.6761 (OUTLIER) cc_final: 0.5798 (pmm) REVERT: B 19 CYS cc_start: 0.6577 (m) cc_final: 0.6306 (p) REVERT: B 21 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7189 (mm) REVERT: B 40 PHE cc_start: 0.7860 (p90) cc_final: 0.7598 (OUTLIER) REVERT: B 80 MET cc_start: 0.8139 (mtp) cc_final: 0.7784 (mtp) REVERT: B 244 LYS cc_start: 0.7220 (mtpp) cc_final: 0.6740 (tttp) REVERT: B 281 GLU cc_start: 0.7397 (pm20) cc_final: 0.7176 (pm20) outliers start: 31 outliers final: 19 residues processed: 206 average time/residue: 0.6112 time to fit residues: 133.8161 Evaluate side-chains 214 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 505 GLN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain B residue 598 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 34 optimal weight: 0.5980 chunk 85 optimal weight: 0.0970 chunk 64 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 113 optimal weight: 0.2980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 215 GLN B 442 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.154928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.137818 restraints weight = 12068.298| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.44 r_work: 0.3662 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 1.8942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9146 Z= 0.158 Angle : 0.702 11.289 12414 Z= 0.350 Chirality : 0.047 0.241 1409 Planarity : 0.007 0.060 1592 Dihedral : 4.953 39.047 1191 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.87 % Allowed : 30.53 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -0.73 (0.25), residues: 1104 helix: 0.80 (0.40), residues: 177 sheet: 0.14 (0.28), residues: 347 loop : -1.30 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 484 TYR 0.017 0.001 TYR B 96 PHE 0.028 0.002 PHE A 515 TRP 0.027 0.002 TRP B 233 HIS 0.003 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 ( 9146) covalent geometry : angle 0.70195 / 0.35 (12414) hydrogen bonds : bond 0.04267 / 2.91 ( 257) hydrogen bonds : angle 5.11962 / 3.47 ( 669) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 196 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 SER cc_start: 0.8391 (m) cc_final: 0.7808 (t) REVERT: A 244 LYS cc_start: 0.7524 (ptpp) cc_final: 0.7157 (tppt) REVERT: A 325 THR cc_start: 0.5514 (m) cc_final: 0.5194 (p) REVERT: A 500 LEU cc_start: 0.7535 (mt) cc_final: 0.7235 (tt) REVERT: A 505 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8325 (tm-30) REVERT: A 514 LEU cc_start: 0.6965 (OUTLIER) cc_final: 0.6743 (tm) REVERT: A 525 LYS cc_start: 0.8160 (mtmt) cc_final: 0.7759 (mtmm) REVERT: A 618 SER cc_start: 0.8091 (t) cc_final: 0.7664 (p) REVERT: B 21 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7254 (mm) REVERT: B 40 PHE cc_start: 0.8044 (p90) cc_final: 0.7724 (OUTLIER) REVERT: B 180 MET cc_start: 0.6981 (mmm) cc_final: 0.6652 (mmt) REVERT: B 281 GLU cc_start: 0.7641 (pm20) cc_final: 0.7404 (pm20) REVERT: B 333 LYS cc_start: 0.7415 (mttm) cc_final: 0.7183 (mttm) REVERT: B 503 GLU cc_start: 0.7357 (tp30) cc_final: 0.6942 (tp30) REVERT: B 509 HIS cc_start: 0.7871 (OUTLIER) cc_final: 0.7226 (p90) outliers start: 29 outliers final: 17 residues processed: 211 average time/residue: 0.5609 time to fit residues: 126.1324 Evaluate side-chains 213 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 505 GLN Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain B residue 598 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 81 optimal weight: 0.8980 chunk 93 optimal weight: 0.0980 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 215 GLN B 442 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.153436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.136291 restraints weight = 11946.489| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.44 r_work: 0.3645 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 1.9174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9146 Z= 0.193 Angle : 0.736 12.541 12414 Z= 0.370 Chirality : 0.048 0.203 1409 Planarity : 0.007 0.062 1592 Dihedral : 5.113 36.554 1191 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.67 % Allowed : 31.32 % Favored : 66.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -0.70 (0.25), residues: 1104 helix: 0.75 (0.40), residues: 177 sheet: 0.15 (0.28), residues: 358 loop : -1.27 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 484 TYR 0.020 0.002 TYR B 96 PHE 0.037 0.002 PHE A 515 TRP 0.033 0.003 TRP B 233 HIS 0.004 0.001 HIS A 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.19 ( 9146) covalent geometry : angle 0.73619 / 0.37 (12414) hydrogen bonds : bond 0.04729 / 3.21 ( 257) hydrogen bonds : angle 5.32629 / 3.62 ( 669) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 LYS cc_start: 0.7562 (ptpp) cc_final: 0.7228 (tppt) REVERT: A 325 THR cc_start: 0.5687 (m) cc_final: 0.5368 (p) REVERT: A 500 LEU cc_start: 0.7576 (mt) cc_final: 0.7274 (tt) REVERT: A 505 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8269 (tm-30) REVERT: A 525 LYS cc_start: 0.8219 (mtmt) cc_final: 0.7816 (mtmm) REVERT: A 589 MET cc_start: 0.7045 (pmm) cc_final: 0.6295 (pmm) REVERT: A 618 SER cc_start: 0.8124 (t) cc_final: 0.7701 (p) REVERT: B 40 PHE cc_start: 0.8047 (p90) cc_final: 0.7726 (p90) REVERT: B 244 LYS cc_start: 0.7288 (mtpp) cc_final: 0.6816 (tttp) REVERT: B 281 GLU cc_start: 0.7692 (pm20) cc_final: 0.7456 (pm20) REVERT: B 333 LYS cc_start: 0.7419 (mttm) cc_final: 0.7047 (mttp) REVERT: B 406 SER cc_start: 0.8025 (p) cc_final: 0.7574 (m) REVERT: B 503 GLU cc_start: 0.7377 (tp30) cc_final: 0.6974 (tp30) REVERT: B 509 HIS cc_start: 0.7972 (OUTLIER) cc_final: 0.7413 (p90) REVERT: B 616 VAL cc_start: 0.8009 (m) cc_final: 0.7784 (p) outliers start: 27 outliers final: 19 residues processed: 207 average time/residue: 0.5046 time to fit residues: 111.4581 Evaluate side-chains 206 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 505 GLN Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 600 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 92 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 69 optimal weight: 0.0370 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 442 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.153346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.136129 restraints weight = 11977.389| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.46 r_work: 0.3637 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 1.9265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9146 Z= 0.194 Angle : 0.746 12.287 12414 Z= 0.371 Chirality : 0.048 0.158 1409 Planarity : 0.007 0.064 1592 Dihedral : 5.133 35.877 1191 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.47 % Allowed : 31.23 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -0.67 (0.25), residues: 1104 helix: 0.75 (0.39), residues: 178 sheet: 0.21 (0.28), residues: 345 loop : -1.25 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 484 TYR 0.019 0.002 TYR B 96 PHE 0.031 0.002 PHE A 515 TRP 0.041 0.003 TRP B 233 HIS 0.005 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.19 ( 9146) covalent geometry : angle 0.74585 / 0.37 (12414) hydrogen bonds : bond 0.04675 / 3.16 ( 257) hydrogen bonds : angle 5.28072 / 3.59 ( 669) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3074.77 seconds wall clock time: 53 minutes 17.69 seconds (3197.69 seconds total)