Starting phenix.real_space_refine on Wed Feb 4 06:32:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9huh_52413/02_2026/9huh_52413.cif Found real_map, /net/cci-nas-00/data/ceres_data/9huh_52413/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9huh_52413/02_2026/9huh_52413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9huh_52413/02_2026/9huh_52413.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9huh_52413/02_2026/9huh_52413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9huh_52413/02_2026/9huh_52413.map" } 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-2.0-5952/lib/python3.9/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, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 2.14, 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: 0.46 Conformation dependent library (CDL) restraints added in 255.0 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: 0.28 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: 1.22 Time building geometry restraints manager: 0.66 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 2.510 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: 6.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.480 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: 0.000 Load rotamer database and sin/cos tables:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2137 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 covalent geometry : bond 0.00981 ( 9146) covalent geometry : angle 1.35073 (12414) hydrogen bonds : bond 0.20931 ( 257) hydrogen bonds : angle 7.84715 ( 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 : 0.275 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 328 MET cc_start: 0.3802 (OUTLIER) cc_final: 0.3511 (mmm) REVERT: B 479 VAL cc_start: -0.0323 (OUTLIER) cc_final: -0.1968 (t) outliers start: 34 outliers final: 3 residues processed: 115 average time/residue: 0.3620 time to fit residues: 45.6545 Evaluate side-chains 79 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 328 MET 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: 0.6980 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... Flipped N/Q/H residues before XYZ refinement: A 26 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 HIS A 276 ASN A 358 GLN A 361 HIS A 444 HIS A 448 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 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.185822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.170351 restraints weight = 12884.904| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 2.36 r_work: 0.4032 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4214 moved from start: 0.6214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 9146 Z= 0.261 Angle : 0.967 15.596 12414 Z= 0.494 Chirality : 0.056 0.283 1409 Planarity : 0.008 0.062 1592 Dihedral : 6.617 41.148 1201 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 5.43 % Allowed : 21.15 % Favored : 73.42 % 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: -2.30 (0.23), residues: 1104 helix: -1.01 (0.36), residues: 190 sheet: -0.73 (0.28), residues: 338 loop : -2.24 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 488 TYR 0.027 0.003 TYR A 250 PHE 0.027 0.003 PHE A 249 TRP 0.026 0.004 TRP A 141 HIS 0.016 0.003 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00576 ( 9146) covalent geometry : angle 0.96675 (12414) hydrogen bonds : bond 0.05449 ( 257) hydrogen bonds : angle 6.42704 ( 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 177 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 122 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 PHE cc_start: 0.5945 (OUTLIER) cc_final: 0.5637 (t80) REVERT: A 538 HIS cc_start: 0.7730 (m170) cc_final: 0.7483 (m170) REVERT: B 67 THR cc_start: 0.6884 (p) cc_final: 0.6497 (p) outliers start: 55 outliers final: 18 residues processed: 161 average time/residue: 0.3431 time to fit residues: 60.6210 Evaluate side-chains 129 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 514 LEU Chi-restraints excluded: chain A residue 515 PHE 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 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: 2.9990 chunk 33 optimal weight: 0.2980 chunk 27 optimal weight: 0.0570 chunk 12 optimal weight: 0.2980 chunk 37 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 51 optimal weight: 0.0000 chunk 43 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 overall best weight: 0.2502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 276 ASN A 505 GLN B 215 GLN B 442 GLN B 455 GLN B 471 HIS B 595 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.177965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.162716 restraints weight = 12702.498| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 2.33 r_work: 0.3990 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5080 moved from start: 0.8383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9146 Z= 0.153 Angle : 0.694 15.393 12414 Z= 0.348 Chirality : 0.046 0.160 1409 Planarity : 0.006 0.052 1592 Dihedral : 4.903 56.743 1191 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 5.63 % Allowed : 21.94 % Favored : 72.43 % 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: -1.78 (0.24), residues: 1104 helix: -0.24 (0.36), residues: 188 sheet: -0.48 (0.29), residues: 326 loop : -1.94 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 8 TYR 0.022 0.002 TYR B 109 PHE 0.012 0.002 PHE A 515 TRP 0.024 0.003 TRP B 233 HIS 0.009 0.002 HIS B 595 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9146) covalent geometry : angle 0.69396 (12414) hydrogen bonds : bond 0.04292 ( 257) hydrogen bonds : angle 5.37621 ( 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 205 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 148 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 THR cc_start: 0.5274 (m) cc_final: 0.4673 (p) REVERT: A 454 GLN cc_start: 0.3318 (OUTLIER) cc_final: 0.3017 (mp10) REVERT: A 631 ASN cc_start: 0.7032 (m-40) cc_final: 0.6792 (p0) REVERT: B 42 ILE cc_start: 0.6939 (OUTLIER) cc_final: 0.6293 (mt) REVERT: B 149 ILE cc_start: 0.6210 (mp) cc_final: 0.6002 (mm) REVERT: B 212 ARG cc_start: 0.7267 (ptp90) cc_final: 0.7024 (ptp-170) REVERT: B 287 ASP cc_start: 0.7095 (t0) cc_final: 0.6239 (t0) REVERT: B 650 ARG cc_start: 0.6921 (tmm-80) cc_final: 0.6718 (ttm170) REVERT: B 661 MET cc_start: 0.2542 (tpt) cc_final: 0.1994 (ttt) outliers start: 57 outliers final: 18 residues processed: 189 average time/residue: 0.3613 time to fit residues: 74.4778 Evaluate side-chains 153 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 454 GLN 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 577 SER Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 454 GLN Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 627 CYS 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: 1.9990 chunk 83 optimal weight: 0.0020 chunk 94 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 67 optimal weight: 0.3980 chunk 85 optimal weight: 0.6980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 136 GLN A 444 HIS A 448 GLN ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.176681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.160114 restraints weight = 12730.640| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 2.40 r_work: 0.3947 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 1.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 9146 Z= 0.262 Angle : 0.883 17.646 12414 Z= 0.449 Chirality : 0.051 0.235 1409 Planarity : 0.007 0.055 1592 Dihedral : 6.024 55.740 1191 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 6.32 % Allowed : 21.74 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.97 (0.24), residues: 1104 helix: -0.08 (0.38), residues: 187 sheet: -0.52 (0.29), residues: 320 loop : -2.23 (0.22), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 441 TYR 0.023 0.003 TYR B 391 PHE 0.023 0.003 PHE A 407 TRP 0.032 0.003 TRP B 233 HIS 0.010 0.002 HIS B 538 Details of bonding type rmsd covalent geometry : bond 0.00557 ( 9146) covalent geometry : angle 0.88278 (12414) hydrogen bonds : bond 0.04981 ( 257) hydrogen bonds : angle 6.04024 ( 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 290 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 226 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 27 LEU cc_start: 0.6160 (OUTLIER) cc_final: 0.5768 (tp) REVERT: A 67 THR cc_start: 0.6883 (OUTLIER) cc_final: 0.6525 (p) REVERT: A 183 MET cc_start: 0.6852 (tpp) cc_final: 0.6404 (ttt) REVERT: A 213 VAL cc_start: 0.6495 (OUTLIER) cc_final: 0.6154 (t) REVERT: A 233 TRP cc_start: 0.8028 (m-90) cc_final: 0.7752 (m-90) REVERT: A 244 LYS cc_start: 0.6451 (OUTLIER) cc_final: 0.5892 (mttp) REVERT: A 299 THR cc_start: 0.8506 (m) cc_final: 0.7862 (p) REVERT: A 461 LYS cc_start: 0.7782 (mtpt) cc_final: 0.7385 (mtpt) REVERT: A 547 ASP cc_start: 0.7394 (m-30) cc_final: 0.7140 (m-30) REVERT: A 550 ARG cc_start: 0.8305 (ttt90) cc_final: 0.7992 (ttt180) REVERT: A 631 ASN cc_start: 0.7513 (m-40) cc_final: 0.7219 (p0) REVERT: A 657 LYS cc_start: 0.7785 (mmtp) cc_final: 0.7560 (mppt) REVERT: B 67 THR cc_start: 0.8153 (p) cc_final: 0.7922 (t) REVERT: B 78 LEU cc_start: 0.7636 (mm) cc_final: 0.7422 (tp) REVERT: B 97 TYR cc_start: 0.5315 (OUTLIER) cc_final: 0.4690 (p90) REVERT: B 249 PHE cc_start: 0.7236 (m-80) cc_final: 0.7008 (m-80) REVERT: B 266 THR cc_start: 0.8079 (t) cc_final: 0.7857 (m) REVERT: B 354 ILE cc_start: 0.7075 (OUTLIER) cc_final: 0.6838 (pp) REVERT: B 432 ASP cc_start: 0.7833 (p0) cc_final: 0.7446 (p0) REVERT: B 662 VAL cc_start: 0.8038 (OUTLIER) cc_final: 0.7776 (m) outliers start: 64 outliers final: 13 residues processed: 269 average time/residue: 0.3900 time to fit residues: 113.1265 Evaluate side-chains 218 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 454 GLN Chi-restraints excluded: chain B residue 582 PHE Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 662 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 109 optimal weight: 0.8980 chunk 27 optimal weight: 0.0030 chunk 55 optimal weight: 0.0070 chunk 36 optimal weight: 0.4980 chunk 111 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 49 optimal weight: 0.3980 chunk 89 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.3208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 GLN B 16 HIS B 196 ASN B 236 HIS B 448 GLN B 505 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.167726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.150446 restraints weight = 12412.213| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.53 r_work: 0.3816 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 1.5579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9146 Z= 0.147 Angle : 0.683 8.376 12414 Z= 0.341 Chirality : 0.046 0.152 1409 Planarity : 0.006 0.066 1592 Dihedral : 4.895 53.426 1191 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.05 % Allowed : 25.69 % Favored : 70.26 % 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: -1.33 (0.24), residues: 1104 helix: 0.52 (0.39), residues: 189 sheet: -0.31 (0.28), residues: 337 loop : -1.75 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 484 TYR 0.009 0.001 TYR B 96 PHE 0.015 0.002 PHE B 368 TRP 0.013 0.002 TRP B 233 HIS 0.007 0.001 HIS B 471 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9146) covalent geometry : angle 0.68344 (12414) hydrogen bonds : bond 0.03970 ( 257) hydrogen bonds : angle 5.14362 ( 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: 41 poor density : 226 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LEU cc_start: 0.6363 (OUTLIER) cc_final: 0.6068 (tp) REVERT: A 244 LYS cc_start: 0.6510 (ptpp) cc_final: 0.6049 (mttp) REVERT: A 328 MET cc_start: 0.5342 (pmt) cc_final: 0.5124 (pmt) REVERT: A 352 MET cc_start: 0.6106 (tmm) cc_final: 0.5495 (tmm) REVERT: A 505 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7296 (tt0) REVERT: A 514 LEU cc_start: 0.6459 (OUTLIER) cc_final: 0.6201 (tm) REVERT: A 525 LYS cc_start: 0.7567 (mtmt) cc_final: 0.7338 (mtmm) REVERT: A 547 ASP cc_start: 0.7742 (m-30) cc_final: 0.7427 (m-30) REVERT: A 550 ARG cc_start: 0.8333 (ttt90) cc_final: 0.8017 (ttt180) REVERT: A 589 MET cc_start: 0.6254 (pp-130) cc_final: 0.5823 (pp-130) REVERT: A 657 LYS cc_start: 0.7769 (mmtp) cc_final: 0.7560 (mmtt) REVERT: B 232 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.7044 (ptpp) REVERT: B 233 TRP cc_start: 0.7728 (m-90) cc_final: 0.7488 (m-90) REVERT: B 244 LYS cc_start: 0.7304 (mtpp) cc_final: 0.6712 (tttp) REVERT: B 368 PHE cc_start: 0.7140 (t80) cc_final: 0.6878 (t80) REVERT: B 495 ARG cc_start: 0.7639 (tpp80) cc_final: 0.7165 (ttt90) REVERT: B 555 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7273 (ttm110) REVERT: B 657 LYS cc_start: 0.7277 (mmpt) cc_final: 0.7038 (mmtm) outliers start: 41 outliers final: 12 residues processed: 246 average time/residue: 0.4376 time to fit residues: 115.6955 Evaluate side-chains 227 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 210 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 505 GLN Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 555 ARG Chi-restraints excluded: chain B residue 582 PHE Chi-restraints excluded: chain B residue 627 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 69 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 98 optimal weight: 0.0970 chunk 71 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 53 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 87 optimal weight: 0.2980 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 GLN B 90 GLN B 196 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.165058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.147458 restraints weight = 12362.204| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.48 r_work: 0.3774 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 1.6640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9146 Z= 0.136 Angle : 0.669 9.841 12414 Z= 0.334 Chirality : 0.045 0.159 1409 Planarity : 0.006 0.052 1592 Dihedral : 4.679 46.225 1191 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 5.34 % Allowed : 26.58 % Favored : 68.08 % 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 are not related in a simple way. whole: -0.96 (0.25), residues: 1104 helix: 0.88 (0.39), residues: 184 sheet: -0.07 (0.29), residues: 334 loop : -1.51 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 484 TYR 0.011 0.001 TYR B 96 PHE 0.017 0.002 PHE B 368 TRP 0.047 0.002 TRP A 233 HIS 0.003 0.001 HIS B 471 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9146) covalent geometry : angle 0.66862 (12414) hydrogen bonds : bond 0.03931 ( 257) hydrogen bonds : angle 4.91033 ( 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 281 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 227 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.8020 (ttm110) cc_final: 0.7762 (ttm170) REVERT: A 25 THR cc_start: 0.8351 (t) cc_final: 0.8114 (p) REVERT: A 67 THR cc_start: 0.7262 (OUTLIER) cc_final: 0.7061 (p) REVERT: A 244 LYS cc_start: 0.6774 (ptpp) cc_final: 0.6293 (mttp) REVERT: A 308 VAL cc_start: 0.7502 (m) cc_final: 0.7261 (t) REVERT: A 352 MET cc_start: 0.6101 (tmm) cc_final: 0.5734 (tmm) REVERT: A 514 LEU cc_start: 0.6602 (OUTLIER) cc_final: 0.6361 (tm) REVERT: A 525 LYS cc_start: 0.7767 (mtmt) cc_final: 0.7529 (mtmm) REVERT: A 550 ARG cc_start: 0.8390 (ttt90) cc_final: 0.8100 (ttt180) REVERT: B 28 ASP cc_start: 0.7220 (t0) cc_final: 0.6951 (t0) REVERT: B 78 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7299 (mp) REVERT: B 232 LYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6718 (ptpp) REVERT: B 233 TRP cc_start: 0.7595 (m-90) cc_final: 0.7272 (m-90) REVERT: B 244 LYS cc_start: 0.7272 (mtpp) cc_final: 0.6775 (tttp) REVERT: B 433 SER cc_start: 0.8172 (p) cc_final: 0.7899 (t) REVERT: B 495 ARG cc_start: 0.7764 (tpp80) cc_final: 0.7497 (ttt180) REVERT: B 555 ARG cc_start: 0.7888 (ttm110) cc_final: 0.7622 (ttm110) REVERT: B 563 ASP cc_start: 0.8009 (m-30) cc_final: 0.7802 (m-30) outliers start: 54 outliers final: 16 residues processed: 261 average time/residue: 0.4236 time to fit residues: 118.4849 Evaluate side-chains 235 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 215 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 78 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 212 ARG Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 627 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 58 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 113 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 43 optimal weight: 0.0040 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 26 GLN B 90 GLN B 196 ASN B 438 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.157351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.139800 restraints weight = 12166.613| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.44 r_work: 0.3672 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 1.7991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9146 Z= 0.208 Angle : 0.748 9.279 12414 Z= 0.379 Chirality : 0.048 0.154 1409 Planarity : 0.007 0.076 1592 Dihedral : 5.223 53.187 1191 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.85 % Allowed : 27.37 % Favored : 68.77 % 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: -1.01 (0.25), residues: 1104 helix: 0.93 (0.39), residues: 175 sheet: 0.04 (0.28), residues: 347 loop : -1.67 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 205 TYR 0.018 0.002 TYR B 96 PHE 0.018 0.002 PHE A 194 TRP 0.047 0.003 TRP A 233 HIS 0.006 0.001 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 9146) covalent geometry : angle 0.74832 (12414) hydrogen bonds : bond 0.05124 ( 257) hydrogen bonds : angle 5.34935 ( 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 250 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 211 time to evaluate : 0.359 Fit side-chains REVERT: A 8 ARG cc_start: 0.8122 (ttm110) cc_final: 0.7788 (mtt180) REVERT: A 28 ASP cc_start: 0.7078 (t0) cc_final: 0.6863 (t0) REVERT: A 232 LYS cc_start: 0.7142 (ptpp) cc_final: 0.6873 (pmtt) REVERT: A 244 LYS cc_start: 0.7108 (ptpp) cc_final: 0.6742 (mttp) REVERT: A 247 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7253 (mtp) REVERT: A 410 LEU cc_start: 0.7963 (mp) cc_final: 0.7762 (mt) REVERT: A 551 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: A 596 LEU cc_start: 0.8063 (mt) cc_final: 0.7856 (mp) REVERT: A 612 LEU cc_start: 0.7718 (mp) cc_final: 0.7475 (mt) REVERT: B 40 PHE cc_start: 0.7831 (p90) cc_final: 0.7607 (p90) REVERT: B 232 LYS cc_start: 0.7091 (OUTLIER) cc_final: 0.6839 (ptpp) REVERT: B 233 TRP cc_start: 0.7575 (m-90) cc_final: 0.7226 (m-90) REVERT: B 244 LYS cc_start: 0.7337 (mtpp) cc_final: 0.6739 (tttp) REVERT: B 281 GLU cc_start: 0.7436 (pm20) cc_final: 0.7181 (pm20) REVERT: B 299 THR cc_start: 0.8423 (m) cc_final: 0.8149 (p) REVERT: B 389 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7556 (t80) REVERT: B 495 ARG cc_start: 0.7749 (tpp80) cc_final: 0.7324 (mtt90) REVERT: B 555 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7796 (ttm110) REVERT: B 657 LYS cc_start: 0.7604 (mmpt) cc_final: 0.7340 (mmtp) outliers start: 39 outliers final: 15 residues processed: 234 average time/residue: 0.4499 time to fit residues: 112.7335 Evaluate side-chains 225 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 205 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain A residue 647 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 185 LEU Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 555 ARG Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 627 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 56 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 72 optimal weight: 0.0670 chunk 96 optimal weight: 0.4980 chunk 87 optimal weight: 0.3980 chunk 71 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 GLN B 136 GLN B 442 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.156282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.139301 restraints weight = 12050.464| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.38 r_work: 0.3685 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 1.8350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9146 Z= 0.162 Angle : 0.689 9.383 12414 Z= 0.343 Chirality : 0.046 0.183 1409 Planarity : 0.007 0.063 1592 Dihedral : 4.903 52.873 1191 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.75 % Allowed : 28.85 % Favored : 67.39 % 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: -0.78 (0.25), residues: 1104 helix: 1.10 (0.40), residues: 175 sheet: 0.20 (0.28), residues: 345 loop : -1.52 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 484 TYR 0.016 0.001 TYR A 96 PHE 0.026 0.002 PHE A 515 TRP 0.051 0.003 TRP A 233 HIS 0.014 0.001 HIS A 509 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 9146) covalent geometry : angle 0.68892 (12414) hydrogen bonds : bond 0.04340 ( 257) hydrogen bonds : angle 5.08846 ( 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 252 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 214 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.8327 (ttm110) cc_final: 0.7988 (mtm180) REVERT: A 28 ASP cc_start: 0.7388 (t0) cc_final: 0.7037 (t0) REVERT: A 109 TYR cc_start: 0.7670 (m-80) cc_final: 0.7380 (m-80) REVERT: A 244 LYS cc_start: 0.7266 (ptpp) cc_final: 0.6925 (mttp) REVERT: A 247 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7560 (mtp) REVERT: A 389 PHE cc_start: 0.5590 (OUTLIER) cc_final: 0.5354 (t80) REVERT: A 509 HIS cc_start: 0.7219 (OUTLIER) cc_final: 0.6863 (p-80) REVERT: A 514 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6652 (tm) REVERT: A 525 LYS cc_start: 0.8130 (mtmt) cc_final: 0.7760 (mtmm) REVERT: B 114 GLU cc_start: 0.7049 (tm-30) cc_final: 0.6716 (tm-30) REVERT: B 156 ARG cc_start: 0.1613 (OUTLIER) cc_final: 0.1077 (tmm-80) REVERT: B 244 LYS cc_start: 0.7361 (mtpp) cc_final: 0.6801 (tttp) REVERT: B 281 GLU cc_start: 0.7638 (pm20) cc_final: 0.7359 (pm20) REVERT: B 523 GLN cc_start: 0.6847 (tp-100) cc_final: 0.6605 (tp-100) REVERT: B 555 ARG cc_start: 0.8276 (ttm110) cc_final: 0.7865 (ttm110) REVERT: B 657 LYS cc_start: 0.7787 (mmpt) cc_final: 0.7557 (mmtp) outliers start: 38 outliers final: 21 residues processed: 234 average time/residue: 0.4510 time to fit residues: 112.9316 Evaluate side-chains 240 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 214 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 40 PHE 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 146 GLN Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 389 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 34 optimal weight: 0.0470 chunk 85 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 113 optimal weight: 0.0670 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 GLN B 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.156562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.139192 restraints weight = 12051.963| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.43 r_work: 0.3689 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 1.8530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9146 Z= 0.154 Angle : 0.696 9.008 12414 Z= 0.345 Chirality : 0.046 0.213 1409 Planarity : 0.007 0.060 1592 Dihedral : 4.881 52.152 1191 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.66 % Allowed : 28.95 % Favored : 67.39 % 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: -0.74 (0.25), residues: 1104 helix: 1.17 (0.40), residues: 175 sheet: 0.20 (0.29), residues: 338 loop : -1.47 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 484 TYR 0.014 0.001 TYR A 96 PHE 0.019 0.002 PHE A 515 TRP 0.046 0.002 TRP A 233 HIS 0.014 0.001 HIS A 509 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 9146) covalent geometry : angle 0.69610 (12414) hydrogen bonds : bond 0.04288 ( 257) hydrogen bonds : angle 5.11074 ( 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 252 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 215 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.8217 (ttm110) cc_final: 0.7935 (mtm-85) REVERT: A 28 ASP cc_start: 0.7149 (t0) cc_final: 0.6822 (t0) REVERT: A 93 GLN cc_start: 0.7456 (pp30) cc_final: 0.7156 (pp30) REVERT: A 232 LYS cc_start: 0.6980 (pttm) cc_final: 0.6746 (pttp) REVERT: A 244 LYS cc_start: 0.7206 (ptpp) cc_final: 0.6878 (mttp) REVERT: A 247 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.7193 (mtp) REVERT: A 389 PHE cc_start: 0.5297 (OUTLIER) cc_final: 0.4998 (t80) REVERT: A 509 HIS cc_start: 0.7146 (OUTLIER) cc_final: 0.6339 (p90) REVERT: A 514 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6568 (tm) REVERT: A 525 LYS cc_start: 0.8000 (mtmt) cc_final: 0.7621 (mtmm) REVERT: A 612 LEU cc_start: 0.7651 (mp) cc_final: 0.7414 (mt) REVERT: B 114 GLU cc_start: 0.6890 (tm-30) cc_final: 0.6546 (tm-30) REVERT: B 156 ARG cc_start: 0.1889 (OUTLIER) cc_final: 0.1287 (tmm-80) REVERT: B 574 LYS cc_start: 0.8007 (mmtt) cc_final: 0.7786 (mmmm) REVERT: B 616 VAL cc_start: 0.7723 (p) cc_final: 0.7493 (m) REVERT: B 657 LYS cc_start: 0.7657 (mmpt) cc_final: 0.7404 (mmtp) outliers start: 37 outliers final: 20 residues processed: 239 average time/residue: 0.4706 time to fit residues: 120.1492 Evaluate side-chains 233 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 647 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 156 ARG Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 555 ARG Chi-restraints excluded: chain B residue 582 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 81 optimal weight: 0.3980 chunk 93 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 85 optimal weight: 0.0970 chunk 87 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 0.0980 chunk 110 optimal weight: 0.0570 overall best weight: 0.2496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 GLN B 3 GLN B 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.158477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.141381 restraints weight = 11983.322| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.40 r_work: 0.3720 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3556 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 1.8697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9146 Z= 0.125 Angle : 0.667 8.765 12414 Z= 0.329 Chirality : 0.045 0.177 1409 Planarity : 0.007 0.059 1592 Dihedral : 4.664 50.499 1191 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.67 % Allowed : 30.24 % Favored : 67.09 % 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: -0.63 (0.25), residues: 1104 helix: 1.28 (0.41), residues: 176 sheet: 0.22 (0.28), residues: 350 loop : -1.39 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 484 TYR 0.010 0.001 TYR A 97 PHE 0.023 0.001 PHE A 515 TRP 0.045 0.002 TRP A 233 HIS 0.011 0.001 HIS A 509 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9146) covalent geometry : angle 0.66673 (12414) hydrogen bonds : bond 0.03757 ( 257) hydrogen bonds : angle 4.94292 ( 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 233 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.8375 (ttm110) cc_final: 0.8120 (mtm-85) REVERT: A 28 ASP cc_start: 0.7406 (t0) cc_final: 0.7098 (t0) REVERT: A 93 GLN cc_start: 0.7699 (pp30) cc_final: 0.7361 (pp30) REVERT: A 244 LYS cc_start: 0.7220 (ptpp) cc_final: 0.6872 (mttp) REVERT: A 509 HIS cc_start: 0.7066 (OUTLIER) cc_final: 0.6837 (p-80) REVERT: A 514 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6667 (tm) REVERT: A 525 LYS cc_start: 0.8069 (mtmt) cc_final: 0.7702 (mtmm) REVERT: A 612 LEU cc_start: 0.7696 (mp) cc_final: 0.7420 (mt) REVERT: B 114 GLU cc_start: 0.7003 (tm-30) cc_final: 0.6582 (tm-30) REVERT: B 244 LYS cc_start: 0.7314 (mtpp) cc_final: 0.6830 (tttp) REVERT: B 299 THR cc_start: 0.8438 (m) cc_final: 0.8123 (p) REVERT: B 574 LYS cc_start: 0.8264 (mmtt) cc_final: 0.7978 (tppp) REVERT: B 657 LYS cc_start: 0.7815 (mmpt) cc_final: 0.7566 (mmtp) outliers start: 27 outliers final: 21 residues processed: 222 average time/residue: 0.5023 time to fit residues: 119.1630 Evaluate side-chains 226 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 647 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 185 LEU Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 555 ARG Chi-restraints excluded: chain B residue 582 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 92 optimal weight: 0.6980 chunk 29 optimal weight: 0.0470 chunk 100 optimal weight: 1.9990 chunk 112 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 18 optimal weight: 0.0020 chunk 109 optimal weight: 0.0870 chunk 96 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.2664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 GLN B 196 ASN B 202 HIS B 286 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.157837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.140590 restraints weight = 12103.421| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.44 r_work: 0.3707 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 1.8824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9146 Z= 0.127 Angle : 0.664 9.046 12414 Z= 0.326 Chirality : 0.046 0.189 1409 Planarity : 0.006 0.059 1592 Dihedral : 4.603 47.522 1191 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.87 % Allowed : 30.24 % Favored : 66.90 % 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: -0.49 (0.25), residues: 1104 helix: 1.39 (0.41), residues: 176 sheet: 0.33 (0.29), residues: 332 loop : -1.28 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 484 TYR 0.013 0.001 TYR B 109 PHE 0.018 0.001 PHE A 515 TRP 0.032 0.002 TRP A 233 HIS 0.011 0.001 HIS A 509 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9146) covalent geometry : angle 0.66369 (12414) hydrogen bonds : bond 0.03742 ( 257) hydrogen bonds : angle 4.88912 ( 669) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2601.02 seconds wall clock time: 44 minutes 58.41 seconds (2698.41 seconds total)