Starting phenix.real_space_refine on Sun Aug 9 12:45:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u3l_41866/08_2026/8u3l_41866_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u3l_41866/08_2026/8u3l_41866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u3l_41866/08_2026/8u3l_41866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u3l_41866/08_2026/8u3l_41866.map" model { file = "/net/cci-nas-00/data/ceres_data/8u3l_41866/08_2026/8u3l_41866_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u3l_41866/08_2026/8u3l_41866_trim.cif" } resolution = 3.7 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= 0.003 sd= 0.068 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: 7 Type Number sf(0) Gaussians P 4 5.49 5 S 100 5.16 5 Na 1 4.78 5 C 11452 2.51 5 N 2804 2.21 5 O 3100 1.98 5 H 17492 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34953 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8701 Classifications: {'peptide': 533} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 518} Chain: "D" Number of atoms: 8701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8701 Classifications: {'peptide': 533} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 518} Chain: "B" Number of atoms: 8701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8701 Classifications: {'peptide': 533} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 518} Chain: "C" Number of atoms: 8701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8701 Classifications: {'peptide': 533} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 518} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {' NA': 1, '3PH': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'3PH': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'3PH': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'3PH': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Time building chain proxies: 6.34, per 1000 atoms: 0.18 Number of scatterers: 34953 At special positions: 0 Unit cell: (124.44, 124.44, 115.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 100 16.00 P 4 15.00 Na 1 11.00 O 3100 8.00 N 2804 7.00 C 11452 6.00 H 17492 1.00 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: 3.05 Conformation dependent library (CDL) restraints added in 984.9 milliseconds 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4032 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 4 sheets defined 64.5% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 203 through 211 removed outlier: 3.565A pdb=" N ILE A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 223 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 261 through 269 Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 345 through 354 removed outlier: 3.592A pdb=" N GLN A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 394 through 402 Processing helix chain 'A' and resid 408 through 413 removed outlier: 4.329A pdb=" N LEU A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 454 removed outlier: 3.697A pdb=" N ARG A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ARG A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 500 Processing helix chain 'A' and resid 504 through 509 removed outlier: 4.287A pdb=" N VAL A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 531 Processing helix chain 'A' and resid 536 through 551 Processing helix chain 'A' and resid 552 through 557 removed outlier: 3.926A pdb=" N ARG A 557 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 599 removed outlier: 3.728A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR A 584 " --> pdb=" O PHE A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 655 through 684 removed outlier: 3.681A pdb=" N GLU A 684 " --> pdb=" O ALA A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 711 removed outlier: 3.702A pdb=" N ASN A 695 " --> pdb=" O GLN A 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 211 removed outlier: 3.565A pdb=" N ILE D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 223 Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 250 through 258 Processing helix chain 'D' and resid 261 through 269 Processing helix chain 'D' and resid 286 through 295 Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 345 through 354 removed outlier: 3.592A pdb=" N GLN D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 366 Processing helix chain 'D' and resid 394 through 402 Processing helix chain 'D' and resid 408 through 413 removed outlier: 4.329A pdb=" N LEU D 413 " --> pdb=" O ARG D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 454 removed outlier: 3.697A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LYS D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ARG D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR D 454 " --> pdb=" O ALA D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 500 Processing helix chain 'D' and resid 504 through 509 removed outlier: 4.287A pdb=" N VAL D 508 " --> pdb=" O LYS D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 531 Processing helix chain 'D' and resid 536 through 551 Processing helix chain 'D' and resid 552 through 557 removed outlier: 3.926A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 599 removed outlier: 3.727A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ARG D 579 " --> pdb=" O ARG D 575 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE D 582 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR D 584 " --> pdb=" O PHE D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 639 Processing helix chain 'D' and resid 640 through 642 No H-bonds generated for 'chain 'D' and resid 640 through 642' Processing helix chain 'D' and resid 655 through 684 removed outlier: 3.681A pdb=" N GLU D 684 " --> pdb=" O ALA D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 711 removed outlier: 3.702A pdb=" N ASN D 695 " --> pdb=" O GLN D 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 211 removed outlier: 3.565A pdb=" N ILE B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 223 Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 261 through 269 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 345 through 354 removed outlier: 3.593A pdb=" N GLN B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 408 through 413 removed outlier: 4.329A pdb=" N LEU B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 454 removed outlier: 3.697A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ARG B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 500 Processing helix chain 'B' and resid 504 through 509 removed outlier: 4.287A pdb=" N VAL B 508 " --> pdb=" O LYS B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 531 Processing helix chain 'B' and resid 536 through 551 Processing helix chain 'B' and resid 552 through 557 removed outlier: 3.927A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 599 removed outlier: 3.727A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ARG B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE B 582 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR B 584 " --> pdb=" O PHE B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 639 Processing helix chain 'B' and resid 640 through 642 No H-bonds generated for 'chain 'B' and resid 640 through 642' Processing helix chain 'B' and resid 655 through 684 removed outlier: 3.681A pdb=" N GLU B 684 " --> pdb=" O ALA B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 711 removed outlier: 3.702A pdb=" N ASN B 695 " --> pdb=" O GLN B 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 211 removed outlier: 3.565A pdb=" N ILE C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 223 Processing helix chain 'C' and resid 233 through 237 Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 261 through 269 Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.592A pdb=" N GLN C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 366 Processing helix chain 'C' and resid 394 through 402 Processing helix chain 'C' and resid 408 through 413 removed outlier: 4.329A pdb=" N LEU C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 454 removed outlier: 3.697A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LYS C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ARG C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR C 454 " --> pdb=" O ALA C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 500 Processing helix chain 'C' and resid 504 through 509 removed outlier: 4.287A pdb=" N VAL C 508 " --> pdb=" O LYS C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 531 Processing helix chain 'C' and resid 536 through 551 Processing helix chain 'C' and resid 552 through 557 removed outlier: 3.926A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 599 removed outlier: 3.727A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR C 584 " --> pdb=" O PHE C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 639 Processing helix chain 'C' and resid 640 through 642 No H-bonds generated for 'chain 'C' and resid 640 through 642' Processing helix chain 'C' and resid 655 through 684 removed outlier: 3.681A pdb=" N GLU C 684 " --> pdb=" O ALA C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 711 removed outlier: 3.702A pdb=" N ASN C 695 " --> pdb=" O GLN C 691 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 369 through 374 removed outlier: 5.959A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 369 through 374 removed outlier: 5.959A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 369 through 374 removed outlier: 5.959A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 369 through 374 removed outlier: 5.959A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) 984 hydrogen bonds defined for protein. 2856 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: 7.96 Time building geometry restraints manager: 4.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17248 1.03 - 1.23: 252 1.23 - 1.42: 7632 1.42 - 1.61: 10060 1.61 - 1.81: 172 Bond restraints: 35364 Sorted by residual: bond pdb=" N ARG D 212 " pdb=" H ARG D 212 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.82e+01 bond pdb=" N SER D 278 " pdb=" H SER D 278 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" N SER C 278 " pdb=" H SER C 278 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" N ARG C 212 " pdb=" H ARG C 212 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" N SER C 253 " pdb=" H SER C 253 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.80e+01 ... (remaining 35359 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 63472 2.81 - 5.61: 196 5.61 - 8.42: 12 8.42 - 11.22: 12 11.22 - 14.03: 4 Bond angle restraints: 63696 Sorted by residual: angle pdb=" O13 3PH C 901 " pdb=" P 3PH C 901 " pdb=" O14 3PH C 901 " ideal model delta sigma weight residual 115.01 100.98 14.03 3.00e+00 1.11e-01 2.19e+01 angle pdb=" O13 3PH A 901 " pdb=" P 3PH A 901 " pdb=" O14 3PH A 901 " ideal model delta sigma weight residual 115.01 101.02 13.99 3.00e+00 1.11e-01 2.17e+01 angle pdb=" O13 3PH B 901 " pdb=" P 3PH B 901 " pdb=" O14 3PH B 901 " ideal model delta sigma weight residual 115.01 101.02 13.99 3.00e+00 1.11e-01 2.17e+01 angle pdb=" O13 3PH D 901 " pdb=" P 3PH D 901 " pdb=" O14 3PH D 901 " ideal model delta sigma weight residual 115.01 101.06 13.95 3.00e+00 1.11e-01 2.16e+01 angle pdb=" N GLU A 536 " pdb=" CA GLU A 536 " pdb=" C GLU A 536 " ideal model delta sigma weight residual 113.28 108.63 4.65 1.22e+00 6.72e-01 1.45e+01 ... (remaining 63691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 14888 17.99 - 35.97: 1324 35.97 - 53.96: 313 53.96 - 71.94: 79 71.94 - 89.93: 44 Dihedral angle restraints: 16648 sinusoidal: 8832 harmonic: 7816 Sorted by residual: dihedral pdb=" CA VAL C 415 " pdb=" C VAL C 415 " pdb=" N GLU C 416 " pdb=" CA GLU C 416 " ideal model delta harmonic sigma weight residual -180.00 -163.68 -16.32 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA VAL A 415 " pdb=" C VAL A 415 " pdb=" N GLU A 416 " pdb=" CA GLU A 416 " ideal model delta harmonic sigma weight residual -180.00 -163.68 -16.32 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA VAL B 415 " pdb=" C VAL B 415 " pdb=" N GLU B 416 " pdb=" CA GLU B 416 " ideal model delta harmonic sigma weight residual -180.00 -163.68 -16.32 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 16645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1603 0.026 - 0.051: 636 0.051 - 0.077: 337 0.077 - 0.103: 94 0.103 - 0.128: 34 Chirality restraints: 2704 Sorted by residual: chirality pdb=" CB THR D 258 " pdb=" CA THR D 258 " pdb=" OG1 THR D 258 " pdb=" CG2 THR D 258 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CB THR A 258 " pdb=" CA THR A 258 " pdb=" OG1 THR A 258 " pdb=" CG2 THR A 258 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.13 2.00e-01 2.50e+01 4.00e-01 chirality pdb=" CB THR C 258 " pdb=" CA THR C 258 " pdb=" OG1 THR C 258 " pdb=" CG2 THR C 258 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 2701 not shown) Planarity restraints: 5056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 652 " -0.018 2.00e-02 2.50e+03 1.76e-02 4.65e+00 pdb=" CG ASN C 652 " 0.001 2.00e-02 2.50e+03 pdb=" OD1 ASN C 652 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN C 652 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN C 652 " 0.025 2.00e-02 2.50e+03 pdb="HD22 ASN C 652 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 652 " 0.018 2.00e-02 2.50e+03 1.76e-02 4.63e+00 pdb=" CG ASN A 652 " -0.000 2.00e-02 2.50e+03 pdb=" OD1 ASN A 652 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A 652 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A 652 " -0.025 2.00e-02 2.50e+03 pdb="HD22 ASN A 652 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 652 " 0.018 2.00e-02 2.50e+03 1.74e-02 4.53e+00 pdb=" CG ASN D 652 " -0.000 2.00e-02 2.50e+03 pdb=" OD1 ASN D 652 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN D 652 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN D 652 " -0.025 2.00e-02 2.50e+03 pdb="HD22 ASN D 652 " 0.024 2.00e-02 2.50e+03 ... (remaining 5053 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 4696 2.26 - 2.85: 77231 2.85 - 3.43: 84736 3.43 - 4.02: 111651 4.02 - 4.60: 172352 Nonbonded interactions: 450666 Sorted by model distance: nonbonded pdb=" OE1 GLU C 371 " pdb="HH22 ARG C 743 " model vdw 1.677 2.450 nonbonded pdb=" OE1 GLU B 371 " pdb="HH22 ARG B 743 " model vdw 1.677 2.450 nonbonded pdb=" OE1 GLU A 371 " pdb="HH22 ARG A 743 " model vdw 1.677 2.450 nonbonded pdb=" OE1 GLU D 371 " pdb="HH22 ARG D 743 " model vdw 1.677 2.450 nonbonded pdb=" O SER D 366 " pdb="HH22 ARG D 739 " model vdw 1.691 2.450 ... (remaining 450661 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' and resid 197 through 901) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue 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: 4.860 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: 0.230 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 32.600 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 17872 Z= 0.236 Angle : 0.646 14.026 24172 Z= 0.337 Chirality : 0.037 0.128 2704 Planarity : 0.003 0.028 2984 Dihedral : 15.351 89.928 6492 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.34 (0.19), residues: 2124 helix: 2.45 (0.15), residues: 1280 sheet: None (None), residues: 0 loop : -1.73 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 331 TYR 0.013 0.001 TYR D 565 PHE 0.017 0.001 PHE C 490 TRP 0.006 0.001 TRP B 272 HIS 0.001 0.000 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.24 (17872) covalent geometry : angle 0.64592 / 0.34 (24172) hydrogen bonds : bond 0.14029 / 8.91 ( 984) hydrogen bonds : angle 5.02626 / 3.55 ( 2856) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.2938 time to fit residues: 102.1683 Evaluate side-chains 198 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 GLN D 202 GLN B 202 GLN C 202 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.149874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.098731 restraints weight = 74359.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.103632 restraints weight = 43299.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.105642 restraints weight = 31026.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.107847 restraints weight = 25472.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.109078 restraints weight = 21758.361| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 17872 Z= 0.130 Angle : 0.479 4.524 24172 Z= 0.266 Chirality : 0.035 0.128 2704 Planarity : 0.003 0.029 2984 Dihedral : 5.930 57.658 2436 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.48 % Allowed : 4.88 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.27 (0.19), residues: 2124 helix: 2.38 (0.15), residues: 1296 sheet: -0.53 (0.67), residues: 72 loop : -1.91 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 363 TYR 0.007 0.001 TYR A 653 PHE 0.009 0.001 PHE D 649 TRP 0.005 0.001 TRP D 372 HIS 0.003 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (17872) covalent geometry : angle 0.47872 / 0.27 (24172) hydrogen bonds : bond 0.05768 / 3.88 ( 984) hydrogen bonds : angle 4.15185 / 2.95 ( 2856) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 208 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 ILE cc_start: 0.7616 (mm) cc_final: 0.7406 (tt) REVERT: D 357 ILE cc_start: 0.7622 (mm) cc_final: 0.7412 (tt) REVERT: B 357 ILE cc_start: 0.7626 (mm) cc_final: 0.7411 (tt) REVERT: C 357 ILE cc_start: 0.7625 (mm) cc_final: 0.7412 (tt) outliers start: 9 outliers final: 9 residues processed: 208 average time/residue: 0.3120 time to fit residues: 100.0403 Evaluate side-chains 209 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 200 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 552 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 169 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 186 optimal weight: 0.3980 chunk 110 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 52 optimal weight: 0.0670 chunk 47 optimal weight: 2.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.156015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.116656 restraints weight = 76962.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.115815 restraints weight = 70700.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.117856 restraints weight = 64470.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.119418 restraints weight = 40533.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.120472 restraints weight = 35625.003| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 17872 Z= 0.114 Angle : 0.458 6.655 24172 Z= 0.251 Chirality : 0.034 0.123 2704 Planarity : 0.003 0.033 2984 Dihedral : 5.647 58.887 2436 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.58 % Allowed : 7.64 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.36 (0.19), residues: 2124 helix: 2.45 (0.15), residues: 1296 sheet: -1.08 (0.62), residues: 84 loop : -1.82 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 363 TYR 0.007 0.001 TYR D 653 PHE 0.008 0.001 PHE A 649 TRP 0.003 0.001 TRP D 740 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (17872) covalent geometry : angle 0.45838 / 0.25 (24172) hydrogen bonds : bond 0.05171 / 3.48 ( 984) hydrogen bonds : angle 3.92825 / 2.80 ( 2856) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 200 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7492 (mp) REVERT: B 268 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7474 (mp) REVERT: C 268 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7484 (mp) outliers start: 11 outliers final: 8 residues processed: 200 average time/residue: 0.3033 time to fit residues: 94.4193 Evaluate side-chains 203 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 192 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 503 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 165 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 198 optimal weight: 1.9990 chunk 156 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.149780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.110661 restraints weight = 78180.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.109877 restraints weight = 74446.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.111782 restraints weight = 70738.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.113858 restraints weight = 41423.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.115638 restraints weight = 34579.185| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 17872 Z= 0.262 Angle : 0.567 5.642 24172 Z= 0.320 Chirality : 0.039 0.141 2704 Planarity : 0.004 0.030 2984 Dihedral : 6.239 52.240 2436 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.49 % Allowed : 9.77 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.19), residues: 2124 helix: 2.13 (0.15), residues: 1244 sheet: -1.94 (0.59), residues: 92 loop : -1.94 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 409 TYR 0.016 0.002 TYR B 453 PHE 0.018 0.002 PHE D 649 TRP 0.004 0.001 TRP D 372 HIS 0.002 0.001 HIS C 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.26 (17872) covalent geometry : angle 0.56700 / 0.32 (24172) hydrogen bonds : bond 0.07792 / 5.25 ( 984) hydrogen bonds : angle 4.48421 / 3.21 ( 2856) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7615 (mp) REVERT: D 268 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7580 (mp) REVERT: B 677 MET cc_start: 0.6687 (ttm) cc_final: 0.6486 (ttm) REVERT: C 268 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7612 (mp) outliers start: 28 outliers final: 16 residues processed: 200 average time/residue: 0.2980 time to fit residues: 92.8189 Evaluate side-chains 207 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 552 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 72 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 209 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 190 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.151356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.112055 restraints weight = 77724.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.111148 restraints weight = 72462.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.112606 restraints weight = 73422.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.117957 restraints weight = 41432.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.118058 restraints weight = 29207.231| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 17872 Z= 0.184 Angle : 0.502 4.894 24172 Z= 0.282 Chirality : 0.036 0.119 2704 Planarity : 0.003 0.032 2984 Dihedral : 6.055 54.366 2436 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.70 % Allowed : 11.31 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.91 (0.19), residues: 2124 helix: 2.25 (0.15), residues: 1244 sheet: -1.89 (0.60), residues: 92 loop : -1.92 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 721 TYR 0.012 0.001 TYR D 565 PHE 0.013 0.001 PHE D 649 TRP 0.004 0.001 TRP D 272 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (17872) covalent geometry : angle 0.50190 / 0.28 (24172) hydrogen bonds : bond 0.06744 / 4.55 ( 984) hydrogen bonds : angle 4.23214 / 3.02 ( 2856) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 28 residues processed: 208 average time/residue: 0.2986 time to fit residues: 97.0649 Evaluate side-chains 220 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 593 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 72 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 157 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.152434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.112915 restraints weight = 77725.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.112546 restraints weight = 69218.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.114357 restraints weight = 66365.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.116438 restraints weight = 39609.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.117754 restraints weight = 34040.417| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17872 Z= 0.148 Angle : 0.491 6.123 24172 Z= 0.272 Chirality : 0.035 0.119 2704 Planarity : 0.003 0.031 2984 Dihedral : 5.898 57.374 2436 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.86 % Allowed : 11.73 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.07 (0.19), residues: 2124 helix: 2.40 (0.15), residues: 1244 sheet: -1.86 (0.60), residues: 92 loop : -1.90 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 363 TYR 0.011 0.001 TYR A 565 PHE 0.010 0.001 PHE C 649 TRP 0.007 0.001 TRP D 272 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (17872) covalent geometry : angle 0.49121 / 0.27 (24172) hydrogen bonds : bond 0.06142 / 4.14 ( 984) hydrogen bonds : angle 4.06370 / 2.90 ( 2856) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 204 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 28 residues processed: 220 average time/residue: 0.2929 time to fit residues: 101.1867 Evaluate side-chains 232 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 593 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 124 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 205 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.153016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.113329 restraints weight = 77714.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.111620 restraints weight = 64449.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.113648 restraints weight = 61541.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.114685 restraints weight = 37751.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.116487 restraints weight = 34075.672| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17872 Z= 0.148 Angle : 0.487 6.399 24172 Z= 0.269 Chirality : 0.035 0.119 2704 Planarity : 0.003 0.030 2984 Dihedral : 5.861 59.965 2436 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.75 % Allowed : 12.10 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.12 (0.19), residues: 2124 helix: 2.45 (0.15), residues: 1244 sheet: -1.85 (0.60), residues: 92 loop : -1.89 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 363 TYR 0.010 0.001 TYR B 565 PHE 0.010 0.001 PHE D 649 TRP 0.009 0.001 TRP A 272 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (17872) covalent geometry : angle 0.48666 / 0.27 (24172) hydrogen bonds : bond 0.06023 / 4.06 ( 984) hydrogen bonds : angle 4.00418 / 2.86 ( 2856) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 32 residues processed: 220 average time/residue: 0.2921 time to fit residues: 101.0543 Evaluate side-chains 236 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 593 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 135 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 184 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 133 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 180 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.152870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.113291 restraints weight = 77741.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.113305 restraints weight = 73183.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.115051 restraints weight = 66217.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.116881 restraints weight = 37704.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.117767 restraints weight = 32815.241| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17872 Z= 0.155 Angle : 0.491 7.021 24172 Z= 0.271 Chirality : 0.035 0.118 2704 Planarity : 0.003 0.030 2984 Dihedral : 5.807 56.768 2436 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.91 % Allowed : 11.73 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.12 (0.19), residues: 2124 helix: 2.45 (0.15), residues: 1244 sheet: -1.85 (0.60), residues: 92 loop : -1.89 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 721 TYR 0.010 0.001 TYR A 565 PHE 0.011 0.001 PHE C 649 TRP 0.011 0.001 TRP A 272 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (17872) covalent geometry : angle 0.49081 / 0.27 (24172) hydrogen bonds : bond 0.06089 / 4.11 ( 984) hydrogen bonds : angle 4.00522 / 2.86 ( 2856) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 36 residues processed: 224 average time/residue: 0.2908 time to fit residues: 102.4398 Evaluate side-chains 244 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 208 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 593 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 124 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 164 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.153998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.114593 restraints weight = 77335.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.115185 restraints weight = 70740.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.116663 restraints weight = 65262.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.118707 restraints weight = 36249.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.119418 restraints weight = 31327.413| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17872 Z= 0.131 Angle : 0.479 7.815 24172 Z= 0.261 Chirality : 0.035 0.118 2704 Planarity : 0.003 0.031 2984 Dihedral : 5.563 54.084 2436 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.70 % Allowed : 11.57 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.26 (0.19), residues: 2124 helix: 2.56 (0.15), residues: 1244 sheet: -1.86 (0.60), residues: 92 loop : -1.82 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 363 TYR 0.012 0.001 TYR B 565 PHE 0.009 0.001 PHE D 649 TRP 0.014 0.001 TRP A 272 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (17872) covalent geometry : angle 0.47936 / 0.26 (24172) hydrogen bonds : bond 0.05599 / 3.78 ( 984) hydrogen bonds : angle 3.88028 / 2.77 ( 2856) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 208 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 28 residues processed: 224 average time/residue: 0.2922 time to fit residues: 102.6350 Evaluate side-chains 228 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 593 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 142 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 202 optimal weight: 0.4980 chunk 158 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.153140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.113288 restraints weight = 77663.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.113021 restraints weight = 70732.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.114783 restraints weight = 67863.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.117208 restraints weight = 39787.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.117945 restraints weight = 33504.841| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17872 Z= 0.153 Angle : 0.497 8.487 24172 Z= 0.271 Chirality : 0.035 0.119 2704 Planarity : 0.003 0.030 2984 Dihedral : 5.563 56.144 2436 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.49 % Allowed : 11.73 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.20 (0.19), residues: 2124 helix: 2.52 (0.15), residues: 1244 sheet: -1.86 (0.60), residues: 92 loop : -1.86 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 721 TYR 0.010 0.001 TYR D 565 PHE 0.011 0.001 PHE C 649 TRP 0.015 0.001 TRP B 272 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (17872) covalent geometry : angle 0.49683 / 0.27 (24172) hydrogen bonds : bond 0.05913 / 3.99 ( 984) hydrogen bonds : angle 3.94446 / 2.82 ( 2856) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 28 residues processed: 216 average time/residue: 0.2972 time to fit residues: 100.3475 Evaluate side-chains 232 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 593 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 158 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.153853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.114248 restraints weight = 77225.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.115317 restraints weight = 70561.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.116609 restraints weight = 66820.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.118979 restraints weight = 35982.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.119634 restraints weight = 29959.158| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17872 Z= 0.138 Angle : 0.488 8.547 24172 Z= 0.266 Chirality : 0.035 0.126 2704 Planarity : 0.003 0.031 2984 Dihedral : 5.419 56.413 2436 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.49 % Allowed : 12.21 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.26 (0.19), residues: 2124 helix: 2.58 (0.15), residues: 1244 sheet: -1.85 (0.60), residues: 92 loop : -1.85 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 721 TYR 0.011 0.001 TYR C 565 PHE 0.010 0.001 PHE D 649 TRP 0.017 0.001 TRP B 272 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (17872) covalent geometry : angle 0.48753 / 0.27 (24172) hydrogen bonds : bond 0.05684 / 3.83 ( 984) hydrogen bonds : angle 3.88527 / 2.77 ( 2856) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4591.08 seconds wall clock time: 79 minutes 31.64 seconds (4771.64 seconds total)