Starting phenix.real_space_refine on Mon Jul 6 11:23:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u3l_41866/07_2026/8u3l_41866_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u3l_41866/07_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_41866/07_2026/8u3l_41866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u3l_41866/07_2026/8u3l_41866.map" model { file = "/net/cci-nas-00/data/ceres_data/8u3l_41866/07_2026/8u3l_41866_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u3l_41866/07_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-dev-6108/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, 34 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'3PH': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 5.77, per 1000 atoms: 0.17 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: 2.97 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.71 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: 7.32 Time building geometry restraints manager: 4.23 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: 5.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.220 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 30.420 Find NCS groups from input model: 0.590 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: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.510 ------------------------------------------------------------------------------- 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 : 0.877 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: 0.2746 time to fit residues: 95.2589 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 : 0.932 ------------------------------------------------------------------------------- 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 = 0.149900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.098728 restraints weight = 74394.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.103508 restraints weight = 43201.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.105604 restraints weight = 31152.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.107625 restraints weight = 25522.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.108917 restraints weight = 22069.998| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.0872 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= 0.131 Angle : 0.480 4.559 24172 Z= 0.266 Chirality : 0.035 0.128 2704 Planarity : 0.003 0.029 2984 Dihedral : 5.927 57.544 2436 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.19 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: 1.26 (0.19), residues: 2124 helix: 2.37 (0.15), residues: 1296 sheet: -0.56 (0.67), residues: 72 loop : -1.92 (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 C 565 PHE 0.010 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 0.00283 / 0.13 (17872) covalent geometry : angle 0.47966 / 0.27 (24172) hydrogen bonds : bond 0.05707 / 3.84 ( 984) hydrogen bonds : angle 4.13496 / 2.93 ( 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 : 0.778 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: 0.7621 (mm) cc_final: 0.7411 (tt) REVERT: B 357 ILE cc_start: 0.7623 (mm) cc_final: 0.7410 (tt) REVERT: C 357 ILE cc_start: 0.7626 (mm) cc_final: 0.7410 (tt) outliers start: 9 outliers final: 9 residues processed: 208 average time/residue: 0.2926 time to fit residues: 93.2195 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 : 0.961 ------------------------------------------------------------------------------- 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: 1.9990 chunk 186 optimal weight: 0.9980 chunk 110 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.154001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.115382 restraints weight = 77130.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.114435 restraints weight = 65861.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.116340 restraints weight = 64435.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.118522 restraints weight = 36208.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.119315 restraints weight = 30784.961| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 17872 Z= 0.149 Angle : 0.485 6.333 24172 Z= 0.269 Chirality : 0.035 0.121 2704 Planarity : 0.003 0.033 2984 Dihedral : 6.015 58.655 2436 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.80 % Allowed : 8.12 % Favored : 91.08 % 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: 1.10 (0.19), residues: 2124 helix: 2.28 (0.15), residues: 1296 sheet: -1.70 (0.59), residues: 92 loop : -1.92 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 363 TYR 0.008 0.001 TYR C 453 PHE 0.011 0.001 PHE A 649 TRP 0.003 0.001 TRP B 372 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (17872) covalent geometry : angle 0.48481 / 0.27 (24172) hydrogen bonds : bond 0.05967 / 4.02 ( 984) hydrogen bonds : angle 4.09546 / 2.92 ( 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 215 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 200 time to evaluate : 1.155 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: 0.7715 (OUTLIER) cc_final: 0.7459 (mp) REVERT: B 268 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7459 (mp) REVERT: C 268 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7458 (mp) outliers start: 15 outliers final: 12 residues processed: 200 average time/residue: 0.2794 time to fit residues: 87.0114 Evaluate side-chains 210 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 195 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 A residue 552 MET Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 552 MET 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 B residue 552 MET Chi-restraints excluded: chain C residue 268 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 165 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 198 optimal weight: 1.9990 chunk 156 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.154804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.116005 restraints weight = 77425.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.119917 restraints weight = 75225.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.121823 restraints weight = 50488.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.122549 restraints weight = 32444.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.124952 restraints weight = 28420.500| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 17872 Z= 0.122 Angle : 0.459 5.901 24172 Z= 0.253 Chirality : 0.035 0.119 2704 Planarity : 0.003 0.030 2984 Dihedral : 5.755 56.013 2436 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.49 % Allowed : 8.55 % Favored : 89.97 % 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: 1.45 (0.19), residues: 2124 helix: 2.67 (0.15), residues: 1244 sheet: -1.13 (0.63), residues: 84 loop : -1.75 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 721 TYR 0.010 0.001 TYR A 565 PHE 0.010 0.001 PHE D 720 TRP 0.003 0.001 TRP D 372 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (17872) covalent geometry : angle 0.45882 / 0.25 (24172) hydrogen bonds : bond 0.05442 / 3.67 ( 984) hydrogen bonds : angle 3.92153 / 2.80 ( 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 221 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.817 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: 0.7705 (OUTLIER) cc_final: 0.7468 (mp) REVERT: D 268 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7448 (mp) REVERT: B 268 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7469 (mp) REVERT: C 268 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7465 (mp) outliers start: 28 outliers final: 16 residues processed: 201 average time/residue: 0.2882 time to fit residues: 89.6791 Evaluate side-chains 213 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 503 LEU 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 503 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 503 LEU 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 503 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 72 optimal weight: 4.9990 chunk 61 optimal weight: 0.0770 chunk 158 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 195 optimal weight: 2.9990 chunk 209 optimal weight: 0.4980 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: 0.8942 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.157140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.110716 restraints weight = 75720.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.116084 restraints weight = 39945.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.118214 restraints weight = 26681.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.120460 restraints weight = 21745.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.121691 restraints weight = 18491.724| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17872 Z= 0.105 Angle : 0.451 8.078 24172 Z= 0.245 Chirality : 0.034 0.119 2704 Planarity : 0.003 0.031 2984 Dihedral : 5.457 59.454 2436 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.27 % Allowed : 9.50 % Favored : 89.23 % 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: 1.62 (0.19), residues: 2124 helix: 2.79 (0.15), residues: 1248 sheet: -1.08 (0.65), residues: 84 loop : -1.65 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 575 TYR 0.010 0.001 TYR C 565 PHE 0.007 0.001 PHE D 591 TRP 0.005 0.001 TRP D 272 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (17872) covalent geometry : angle 0.45149 / 0.25 (24172) hydrogen bonds : bond 0.04882 / 3.29 ( 984) hydrogen bonds : angle 3.75597 / 2.68 ( 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 220 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 1.002 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: D 268 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7678 (mp) outliers start: 24 outliers final: 20 residues processed: 204 average time/residue: 0.3236 time to fit residues: 100.3818 Evaluate side-chains 213 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 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 388 ASP Chi-restraints excluded: chain D residue 503 LEU 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 72 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 137 optimal weight: 0.0470 chunk 30 optimal weight: 0.5980 chunk 60 optimal weight: 10.0000 chunk 157 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.8882 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.157868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.118803 restraints weight = 75579.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.119085 restraints weight = 64452.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.120540 restraints weight = 64581.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.123401 restraints weight = 37787.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.123975 restraints weight = 30807.348| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 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 : 0.002 0.026 17872 Z= 0.103 Angle : 0.449 6.632 24172 Z= 0.243 Chirality : 0.034 0.119 2704 Planarity : 0.003 0.031 2984 Dihedral : 5.233 57.644 2436 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.11 % Allowed : 10.14 % 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: 1.69 (0.19), residues: 2124 helix: 2.84 (0.15), residues: 1248 sheet: -1.12 (0.65), residues: 84 loop : -1.61 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 363 TYR 0.010 0.001 TYR B 565 PHE 0.011 0.001 PHE B 720 TRP 0.007 0.001 TRP A 272 HIS 0.002 0.000 HIS C 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (17872) covalent geometry : angle 0.44860 / 0.24 (24172) hydrogen bonds : bond 0.04755 / 3.21 ( 984) hydrogen bonds : angle 3.68424 / 2.63 ( 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 223 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 1.007 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: D 268 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7422 (mp) outliers start: 21 outliers final: 19 residues processed: 210 average time/residue: 0.2942 time to fit residues: 95.8252 Evaluate side-chains 216 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 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 388 ASP Chi-restraints excluded: chain D residue 503 LEU 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 124 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 205 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 114 optimal weight: 0.0060 chunk 76 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 chunk 80 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.158277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.119419 restraints weight = 75615.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.122683 restraints weight = 64259.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.124069 restraints weight = 41196.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.124683 restraints weight = 30682.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.125411 restraints weight = 29802.681| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17872 Z= 0.102 Angle : 0.448 6.915 24172 Z= 0.242 Chirality : 0.034 0.118 2704 Planarity : 0.003 0.032 2984 Dihedral : 4.929 53.620 2436 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.70 % Allowed : 10.03 % Favored : 88.27 % 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: 1.76 (0.19), residues: 2124 helix: 2.89 (0.15), residues: 1248 sheet: -1.13 (0.65), residues: 84 loop : -1.57 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 363 TYR 0.010 0.001 TYR C 565 PHE 0.007 0.001 PHE D 591 TRP 0.008 0.001 TRP A 272 HIS 0.002 0.000 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (17872) covalent geometry : angle 0.44838 / 0.24 (24172) hydrogen bonds : bond 0.04630 / 3.12 ( 984) hydrogen bonds : angle 3.62737 / 2.59 ( 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 238 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 0.779 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: D 268 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7336 (mp) outliers start: 32 outliers final: 27 residues processed: 226 average time/residue: 0.2967 time to fit residues: 102.6852 Evaluate side-chains 224 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 509 ASP Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 268 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 509 ASP 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 509 ASP 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 509 ASP 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: 6.9990 chunk 184 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 183 optimal weight: 0.5980 chunk 180 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.156447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.117476 restraints weight = 75818.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.118742 restraints weight = 64733.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.120473 restraints weight = 58297.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.121597 restraints weight = 35115.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.123254 restraints weight = 31862.638| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1633 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= 0.125 Angle : 0.465 6.935 24172 Z= 0.253 Chirality : 0.034 0.118 2704 Planarity : 0.003 0.031 2984 Dihedral : 4.928 49.728 2436 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.70 % Allowed : 9.82 % Favored : 88.48 % 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: 1.65 (0.19), residues: 2124 helix: 2.80 (0.15), residues: 1248 sheet: -1.18 (0.65), residues: 84 loop : -1.60 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 499 TYR 0.009 0.001 TYR C 565 PHE 0.014 0.001 PHE B 720 TRP 0.010 0.001 TRP B 272 HIS 0.002 0.000 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (17872) covalent geometry : angle 0.46507 / 0.25 (24172) hydrogen bonds : bond 0.05131 / 3.46 ( 984) hydrogen bonds : angle 3.71612 / 2.65 ( 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 230 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.930 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: D 268 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7439 (mp) outliers start: 32 outliers final: 31 residues processed: 214 average time/residue: 0.2771 time to fit residues: 92.3404 Evaluate side-chains 230 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 507 PHE Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 268 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 507 PHE Chi-restraints excluded: chain D residue 509 ASP 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 507 PHE Chi-restraints excluded: chain B residue 509 ASP 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 507 PHE Chi-restraints excluded: chain C residue 509 ASP 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: 0.9990 chunk 50 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 164 optimal weight: 0.8980 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.3944 r_free = 0.3944 target = 0.157316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.118468 restraints weight = 75448.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.117392 restraints weight = 65148.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.119860 restraints weight = 59830.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.120409 restraints weight = 37925.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.122577 restraints weight = 34723.845| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17872 Z= 0.112 Angle : 0.458 7.957 24172 Z= 0.248 Chirality : 0.034 0.118 2704 Planarity : 0.003 0.032 2984 Dihedral : 4.690 43.425 2436 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.75 % Allowed : 10.19 % Favored : 88.06 % 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: 1.73 (0.19), residues: 2124 helix: 2.86 (0.15), residues: 1248 sheet: -1.13 (0.65), residues: 84 loop : -1.58 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 721 TYR 0.009 0.001 TYR A 565 PHE 0.007 0.001 PHE B 649 TRP 0.011 0.001 TRP C 272 HIS 0.002 0.000 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (17872) covalent geometry : angle 0.45788 / 0.25 (24172) hydrogen bonds : bond 0.04901 / 3.30 ( 984) hydrogen bonds : angle 3.65929 / 2.61 ( 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 231 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 1.010 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: 214 average time/residue: 0.2794 time to fit residues: 92.1595 Evaluate side-chains 226 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 507 PHE Chi-restraints excluded: chain A residue 509 ASP 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 507 PHE Chi-restraints excluded: chain D residue 509 ASP 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 507 PHE Chi-restraints excluded: chain B residue 509 ASP 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 507 PHE Chi-restraints excluded: chain C residue 509 ASP 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: 10.0000 chunk 202 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 171 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.152825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.114099 restraints weight = 77663.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.118335 restraints weight = 78886.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.120182 restraints weight = 51628.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.120831 restraints weight = 33587.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.122943 restraints weight = 29154.346| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17872 Z= 0.186 Angle : 0.519 8.336 24172 Z= 0.286 Chirality : 0.036 0.119 2704 Planarity : 0.003 0.031 2984 Dihedral : 5.440 56.430 2436 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.65 % Allowed : 10.46 % Favored : 87.90 % 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: 1.33 (0.19), residues: 2124 helix: 2.55 (0.15), residues: 1248 sheet: -1.78 (0.61), residues: 92 loop : -1.68 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 721 TYR 0.011 0.001 TYR C 453 PHE 0.018 0.001 PHE B 720 TRP 0.014 0.001 TRP D 272 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (17872) covalent geometry : angle 0.51926 / 0.29 (24172) hydrogen bonds : bond 0.06331 / 4.26 ( 984) hydrogen bonds : angle 3.99121 / 2.85 ( 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 226 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 0.988 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: 31 outliers final: 27 residues processed: 211 average time/residue: 0.2804 time to fit residues: 92.1077 Evaluate side-chains 222 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 509 ASP 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 509 ASP 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 509 ASP 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 509 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 158 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 182 optimal weight: 0.0270 chunk 174 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.156542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.117651 restraints weight = 75400.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.119502 restraints weight = 64689.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.122810 restraints weight = 44662.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.122811 restraints weight = 31161.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.123265 restraints weight = 29429.942| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17872 Z= 0.111 Angle : 0.468 8.337 24172 Z= 0.253 Chirality : 0.034 0.119 2704 Planarity : 0.003 0.032 2984 Dihedral : 4.785 44.003 2436 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.27 % Allowed : 10.99 % Favored : 87.74 % 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: 1.63 (0.19), residues: 2124 helix: 2.78 (0.15), residues: 1248 sheet: -1.17 (0.64), residues: 84 loop : -1.62 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 363 TYR 0.011 0.001 TYR A 565 PHE 0.007 0.001 PHE C 659 TRP 0.016 0.001 TRP D 272 HIS 0.001 0.000 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (17872) covalent geometry : angle 0.46832 / 0.25 (24172) hydrogen bonds : bond 0.05129 / 3.46 ( 984) hydrogen bonds : angle 3.70528 / 2.64 ( 2856) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4315.74 seconds wall clock time: 74 minutes 33.71 seconds (4473.71 seconds total)