Starting phenix.real_space_refine on Sat Feb 7 16:43:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u3l_41866/02_2026/8u3l_41866_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u3l_41866/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/8u3l_41866/02_2026/8u3l_41866_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u3l_41866/02_2026/8u3l_41866_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u3l_41866/02_2026/8u3l_41866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u3l_41866/02_2026/8u3l_41866.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 4 5.49 5 S 100 5.16 5 Na 1 4.78 5 C 11452 2.51 5 N 2804 2.21 5 O 3100 1.98 5 H 17492 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34953 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8701 Classifications: {'peptide': 533} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 518} Chain: "D" Number of atoms: 8701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8701 Classifications: {'peptide': 533} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 518} Chain: "B" Number of atoms: 8701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8701 Classifications: {'peptide': 533} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 518} Chain: "C" Number of atoms: 8701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8701 Classifications: {'peptide': 533} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 518} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {' NA': 1, '3PH': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'3PH': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'3PH': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'3PH': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Time building chain proxies: 6.15, per 1000 atoms: 0.18 Number of scatterers: 34953 At special positions: 0 Unit cell: (124.44, 124.44, 115.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 100 16.00 P 4 15.00 Na 1 11.00 O 3100 8.00 N 2804 7.00 C 11452 6.00 H 17492 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 930.6 milliseconds 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4032 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 4 sheets defined 64.5% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 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: 6.94 Time building geometry restraints manager: 4.17 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 - 29.90: 15939 29.90 - 59.80: 685 59.80 - 89.70: 48 89.70 - 119.60: 8 119.60 - 149.50: 4 Dihedral angle restraints: 16684 sinusoidal: 8868 harmonic: 7816 Sorted by residual: dihedral pdb=" C21 3PH C 901 " pdb=" C2 3PH C 901 " pdb=" O21 3PH C 901 " pdb=" C3 3PH C 901 " ideal model delta sinusoidal sigma weight residual 147.58 -62.92 -149.50 1 3.00e+01 1.11e-03 1.99e+01 dihedral pdb=" C21 3PH D 901 " pdb=" C2 3PH D 901 " pdb=" O21 3PH D 901 " pdb=" C3 3PH D 901 " ideal model delta sinusoidal sigma weight residual 147.58 -62.98 -149.44 1 3.00e+01 1.11e-03 1.99e+01 dihedral pdb=" C21 3PH B 901 " pdb=" C2 3PH B 901 " pdb=" O21 3PH B 901 " pdb=" C3 3PH B 901 " ideal model delta sinusoidal sigma weight residual 147.58 -62.98 -149.44 1 3.00e+01 1.11e-03 1.99e+01 ... (remaining 16681 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: 5.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.050 Process input model: 30.610 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 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 : 15.862 149.498 6528 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 covalent geometry : bond 0.00461 (17872) covalent geometry : angle 0.64590 (24172) hydrogen bonds : bond 0.14029 ( 984) hydrogen bonds : angle 5.02626 ( 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 : 0.835 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: 0.2895 time to fit residues: 98.7864 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 : 0.922 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.149859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.098772 restraints weight = 74207.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.103421 restraints weight = 43141.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.105432 restraints weight = 31248.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.107614 restraints weight = 25954.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.108499 restraints weight = 22355.191| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17872 Z= 0.130 Angle : 0.481 4.667 24172 Z= 0.266 Chirality : 0.035 0.128 2704 Planarity : 0.003 0.029 2984 Dihedral : 8.283 138.451 2472 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.27 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: 1.28 (0.19), residues: 2124 helix: 2.38 (0.15), residues: 1296 sheet: -0.50 (0.67), residues: 72 loop : -1.91 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 363 TYR 0.008 0.001 TYR D 653 PHE 0.010 0.001 PHE D 649 TRP 0.004 0.001 TRP D 372 HIS 0.004 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00282 (17872) covalent geometry : angle 0.48107 (24172) hydrogen bonds : bond 0.05765 ( 984) hydrogen bonds : angle 4.16310 ( 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 : 0.904 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: 0.7615 (mm) cc_final: 0.7401 (tt) REVERT: D 357 ILE cc_start: 0.7620 (mm) cc_final: 0.7407 (tt) REVERT: B 357 ILE cc_start: 0.7622 (mm) cc_final: 0.7406 (tt) REVERT: C 357 ILE cc_start: 0.7624 (mm) cc_final: 0.7406 (tt) outliers start: 9 outliers final: 9 residues processed: 208 average time/residue: 0.3094 time to fit residues: 97.5427 Evaluate side-chains 207 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 198 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 552 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 169 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 186 optimal weight: 0.7980 chunk 110 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 201 optimal weight: 0.0980 chunk 117 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.155090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.116323 restraints weight = 77158.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.113979 restraints weight = 67963.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.116242 restraints weight = 64682.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.117996 restraints weight = 39594.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.119033 restraints weight = 34498.023| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1021 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= 0.126 Angle : 0.469 6.443 24172 Z= 0.258 Chirality : 0.035 0.123 2704 Planarity : 0.003 0.032 2984 Dihedral : 7.946 137.379 2472 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.80 % Allowed : 7.48 % Favored : 91.72 % 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: -1.09 (0.62), residues: 84 loop : -1.85 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 363 TYR 0.007 0.001 TYR D 653 PHE 0.009 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 covalent geometry : bond 0.00277 (17872) covalent geometry : angle 0.46910 (24172) hydrogen bonds : bond 0.05505 ( 984) hydrogen bonds : angle 3.99947 ( 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 : 0.895 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: 0.7729 (OUTLIER) cc_final: 0.7474 (mp) REVERT: B 268 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7469 (mp) REVERT: C 268 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7467 (mp) outliers start: 15 outliers final: 12 residues processed: 200 average time/residue: 0.3130 time to fit residues: 95.7875 Evaluate side-chains 207 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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: 10.0000 chunk 81 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 198 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.151471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.112388 restraints weight = 77701.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.110026 restraints weight = 65339.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.112030 restraints weight = 63852.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.113296 restraints weight = 40075.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.114737 restraints weight = 35722.242| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 17872 Z= 0.204 Angle : 0.516 5.282 24172 Z= 0.290 Chirality : 0.037 0.129 2704 Planarity : 0.003 0.030 2984 Dihedral : 8.664 138.177 2472 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.43 % Allowed : 9.24 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.19), residues: 2124 helix: 2.38 (0.15), residues: 1244 sheet: -1.87 (0.60), residues: 92 loop : -1.84 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 409 TYR 0.013 0.001 TYR B 453 PHE 0.015 0.001 PHE C 649 TRP 0.004 0.001 TRP D 372 HIS 0.001 0.000 HIS C 358 Details of bonding type rmsd covalent geometry : bond 0.00475 (17872) covalent geometry : angle 0.51612 (24172) hydrogen bonds : bond 0.06841 ( 984) hydrogen bonds : angle 4.25155 ( 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 223 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 0.896 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: 0.7890 (OUTLIER) cc_final: 0.7659 (mp) REVERT: B 268 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7674 (mp) REVERT: C 268 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7677 (mp) outliers start: 27 outliers final: 19 residues processed: 204 average time/residue: 0.2799 time to fit residues: 87.7706 Evaluate side-chains 218 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 503 LEU Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 552 MET 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 B residue 552 MET Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 552 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 72 optimal weight: 0.3980 chunk 61 optimal weight: 0.1980 chunk 158 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 209 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 190 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.153218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.114190 restraints weight = 77730.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.112471 restraints weight = 73188.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.114011 restraints weight = 73899.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.119392 restraints weight = 42559.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.119434 restraints weight = 30535.775| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 17872 Z= 0.143 Angle : 0.473 5.101 24172 Z= 0.262 Chirality : 0.035 0.119 2704 Planarity : 0.003 0.030 2984 Dihedral : 8.487 133.701 2472 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.70 % Allowed : 10.62 % Favored : 87.69 % 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: 1.21 (0.19), residues: 2124 helix: 2.50 (0.15), residues: 1244 sheet: -1.79 (0.60), residues: 92 loop : -1.82 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 363 TYR 0.012 0.001 TYR A 565 PHE 0.010 0.001 PHE D 649 TRP 0.005 0.001 TRP A 272 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00320 (17872) covalent geometry : angle 0.47277 (24172) hydrogen bonds : bond 0.05946 ( 984) hydrogen bonds : angle 4.01054 ( 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 232 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 0.857 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 677 MET cc_start: 0.6495 (ttm) cc_final: 0.6284 (ttm) REVERT: A 682 MET cc_start: 0.8082 (tmm) cc_final: 0.7845 (tmm) REVERT: D 268 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7513 (mp) REVERT: D 677 MET cc_start: 0.6488 (ttm) cc_final: 0.6280 (ttm) REVERT: D 682 MET cc_start: 0.8099 (tmm) cc_final: 0.7867 (tmm) REVERT: B 677 MET cc_start: 0.6532 (ttm) cc_final: 0.6330 (ttm) REVERT: B 682 MET cc_start: 0.8069 (tmm) cc_final: 0.7839 (tmm) REVERT: C 677 MET cc_start: 0.6545 (ttm) cc_final: 0.6341 (ttm) REVERT: C 682 MET cc_start: 0.8080 (tmm) cc_final: 0.7839 (tmm) outliers start: 32 outliers final: 28 residues processed: 212 average time/residue: 0.2766 time to fit residues: 90.2204 Evaluate side-chains 229 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 509 ASP Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 552 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 72 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 157 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.152042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.113438 restraints weight = 77754.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.118362 restraints weight = 80787.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.120472 restraints weight = 43031.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.121920 restraints weight = 28720.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.122779 restraints weight = 26010.966| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 17872 Z= 0.172 Angle : 0.490 4.320 24172 Z= 0.274 Chirality : 0.036 0.118 2704 Planarity : 0.003 0.030 2984 Dihedral : 8.507 133.799 2472 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.80 % Allowed : 10.93 % Favored : 87.26 % 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: 1.08 (0.19), residues: 2124 helix: 2.40 (0.15), residues: 1244 sheet: -1.80 (0.60), residues: 92 loop : -1.88 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 363 TYR 0.011 0.001 TYR A 565 PHE 0.013 0.001 PHE D 649 TRP 0.007 0.001 TRP B 272 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00396 (17872) covalent geometry : angle 0.48952 (24172) hydrogen bonds : bond 0.06395 ( 984) hydrogen bonds : angle 4.07874 ( 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 237 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 0.788 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: C 682 MET cc_start: 0.8138 (tmm) cc_final: 0.7932 (tmm) outliers start: 34 outliers final: 32 residues processed: 220 average time/residue: 0.2739 time to fit residues: 92.7520 Evaluate side-chains 232 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 509 ASP Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 593 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 124 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.151881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.112495 restraints weight = 77949.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.111476 restraints weight = 73650.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.113509 restraints weight = 67509.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.115270 restraints weight = 41088.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.116275 restraints weight = 35531.850| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 17872 Z= 0.183 Angle : 0.502 5.417 24172 Z= 0.281 Chirality : 0.036 0.118 2704 Planarity : 0.003 0.031 2984 Dihedral : 8.363 132.265 2472 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.12 % Allowed : 11.25 % Favored : 86.62 % 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: 1.03 (0.19), residues: 2124 helix: 2.36 (0.15), residues: 1244 sheet: -1.86 (0.60), residues: 92 loop : -1.90 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 721 TYR 0.010 0.001 TYR B 565 PHE 0.013 0.001 PHE A 649 TRP 0.009 0.001 TRP B 272 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00423 (17872) covalent geometry : angle 0.50166 (24172) hydrogen bonds : bond 0.06551 ( 984) hydrogen bonds : angle 4.11182 ( 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 241 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 201 time to evaluate : 0.891 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: 40 outliers final: 36 residues processed: 224 average time/residue: 0.2720 time to fit residues: 94.6139 Evaluate side-chains 236 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 A residue 552 MET Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 509 ASP Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 593 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 135 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 184 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 180 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.155146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.115738 restraints weight = 77830.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.118890 restraints weight = 72512.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.119632 restraints weight = 62292.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.122487 restraints weight = 34233.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.122745 restraints weight = 28086.662| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 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 : 0.002 0.033 17872 Z= 0.114 Angle : 0.462 7.038 24172 Z= 0.253 Chirality : 0.034 0.119 2704 Planarity : 0.003 0.031 2984 Dihedral : 7.789 125.309 2472 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.49 % Allowed : 11.78 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.19), residues: 2124 helix: 2.68 (0.15), residues: 1244 sheet: -1.76 (0.61), residues: 92 loop : -1.78 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 721 TYR 0.011 0.001 TYR C 565 PHE 0.015 0.001 PHE D 720 TRP 0.012 0.001 TRP A 272 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00245 (17872) covalent geometry : angle 0.46177 (24172) hydrogen bonds : bond 0.05247 ( 984) hydrogen bonds : angle 3.78604 ( 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 232 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 28 residues processed: 220 average time/residue: 0.2906 time to fit residues: 98.3309 Evaluate side-chains 231 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 203 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 503 LEU 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: 4.9990 chunk 141 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 164 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.154631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.115216 restraints weight = 77345.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.118549 restraints weight = 73423.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.119716 restraints weight = 58618.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.122170 restraints weight = 34974.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.122814 restraints weight = 28885.837| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1597 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= 0.123 Angle : 0.466 7.917 24172 Z= 0.256 Chirality : 0.034 0.118 2704 Planarity : 0.003 0.031 2984 Dihedral : 7.613 123.469 2472 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.70 % Allowed : 11.41 % Favored : 86.89 % 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: 1.38 (0.19), residues: 2124 helix: 2.68 (0.15), residues: 1244 sheet: -1.74 (0.61), residues: 92 loop : -1.82 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 721 TYR 0.011 0.001 TYR C 565 PHE 0.009 0.001 PHE A 649 TRP 0.014 0.001 TRP C 272 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00272 (17872) covalent geometry : angle 0.46614 (24172) hydrogen bonds : bond 0.05365 ( 984) hydrogen bonds : angle 3.79764 ( 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 232 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 32 residues processed: 220 average time/residue: 0.2934 time to fit residues: 100.0315 Evaluate side-chains 232 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 A residue 593 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 509 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 593 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 142 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 202 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 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: 0.2980 chunk 112 optimal weight: 0.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.153458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.113663 restraints weight = 77720.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.116394 restraints weight = 74321.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.117723 restraints weight = 61909.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.120181 restraints weight = 36128.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.120884 restraints weight = 29683.612| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1665 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= 0.152 Angle : 0.489 7.944 24172 Z= 0.269 Chirality : 0.035 0.119 2704 Planarity : 0.003 0.031 2984 Dihedral : 7.567 121.941 2472 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.70 % Allowed : 11.62 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.19), residues: 2124 helix: 2.58 (0.15), residues: 1244 sheet: -1.78 (0.61), residues: 92 loop : -1.85 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 721 TYR 0.010 0.001 TYR D 565 PHE 0.011 0.001 PHE B 649 TRP 0.016 0.001 TRP B 272 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00345 (17872) covalent geometry : angle 0.48851 (24172) hydrogen bonds : bond 0.05875 ( 984) hydrogen bonds : angle 3.91322 ( 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 232 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 32 residues processed: 220 average time/residue: 0.3016 time to fit residues: 102.8237 Evaluate side-chains 236 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 A residue 593 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 509 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 593 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 158 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 125 optimal weight: 0.2980 chunk 182 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.154181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.115001 restraints weight = 77372.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.114213 restraints weight = 74316.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.115601 restraints weight = 75305.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.121214 restraints weight = 42173.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.121301 restraints weight = 29009.019| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17872 Z= 0.131 Angle : 0.476 8.101 24172 Z= 0.261 Chirality : 0.035 0.125 2704 Planarity : 0.003 0.031 2984 Dihedral : 7.376 119.267 2472 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.70 % Allowed : 11.78 % Favored : 86.52 % 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: 2.64 (0.15), residues: 1244 sheet: -1.71 (0.61), residues: 92 loop : -1.85 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 721 TYR 0.010 0.001 TYR C 565 PHE 0.009 0.001 PHE B 649 TRP 0.018 0.001 TRP C 272 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00293 (17872) covalent geometry : angle 0.47616 (24172) hydrogen bonds : bond 0.05532 ( 984) hydrogen bonds : angle 3.83170 ( 2856) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4406.89 seconds wall clock time: 76 minutes 17.66 seconds (4577.66 seconds total)