Starting phenix.real_space_refine on Tue Aug 26 08:27:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u3l_41866/08_2025/8u3l_41866_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u3l_41866/08_2025/8u3l_41866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u3l_41866/08_2025/8u3l_41866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u3l_41866/08_2025/8u3l_41866.map" model { file = "/net/cci-nas-00/data/ceres_data/8u3l_41866/08_2025/8u3l_41866_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u3l_41866/08_2025/8u3l_41866_trim.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 4 5.49 5 S 100 5.16 5 Na 1 4.78 5 C 11452 2.51 5 N 2804 2.21 5 O 3100 1.98 5 H 17492 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34953 Number of models: 1 Model: "" Number of chains: 6 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: "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: "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} Restraints were copied for chains: B, C, D Time building chain proxies: 9.03, per 1000 atoms: 0.26 Number of scatterers: 34953 At special positions: 0 Unit cell: (124.44, 124.44, 115.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 100 16.00 P 4 15.00 Na 1 11.00 O 3100 8.00 N 2804 7.00 C 11452 6.00 H 17492 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 900.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 203 through 211 removed outlier: 3.565A pdb=" N ILE A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 223 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 261 through 269 Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 345 through 354 removed outlier: 3.592A pdb=" N GLN A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 394 through 402 Processing helix chain 'A' and resid 408 through 413 removed outlier: 4.329A pdb=" N LEU A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 454 removed outlier: 3.697A pdb=" N ARG A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ARG A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 500 Processing helix chain 'A' and resid 504 through 509 removed outlier: 4.287A pdb=" N VAL A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 531 Processing helix chain 'A' and resid 536 through 551 Processing helix chain 'A' and resid 552 through 557 removed outlier: 3.926A pdb=" N ARG A 557 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 599 removed outlier: 3.728A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR A 584 " --> pdb=" O PHE A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 655 through 684 removed outlier: 3.681A pdb=" N GLU A 684 " --> pdb=" O ALA A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 711 removed outlier: 3.702A pdb=" N ASN A 695 " --> pdb=" O GLN A 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 211 removed outlier: 3.565A pdb=" N ILE D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 223 Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 250 through 258 Processing helix chain 'D' and resid 261 through 269 Processing helix chain 'D' and resid 286 through 295 Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 345 through 354 removed outlier: 3.592A pdb=" N GLN D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 366 Processing helix chain 'D' and resid 394 through 402 Processing helix chain 'D' and resid 408 through 413 removed outlier: 4.329A pdb=" N LEU D 413 " --> pdb=" O ARG D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 454 removed outlier: 3.697A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LYS D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ARG D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR D 454 " --> pdb=" O ALA D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 500 Processing helix chain 'D' and resid 504 through 509 removed outlier: 4.287A pdb=" N VAL D 508 " --> pdb=" O LYS D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 531 Processing helix chain 'D' and resid 536 through 551 Processing helix chain 'D' and resid 552 through 557 removed outlier: 3.926A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 599 removed outlier: 3.727A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ARG D 579 " --> pdb=" O ARG D 575 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE D 582 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR D 584 " --> pdb=" O PHE D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 639 Processing helix chain 'D' and resid 640 through 642 No H-bonds generated for 'chain 'D' and resid 640 through 642' Processing helix chain 'D' and resid 655 through 684 removed outlier: 3.681A pdb=" N GLU D 684 " --> pdb=" O ALA D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 711 removed outlier: 3.702A pdb=" N ASN D 695 " --> pdb=" O GLN D 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 211 removed outlier: 3.565A pdb=" N ILE B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 223 Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 261 through 269 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 345 through 354 removed outlier: 3.593A pdb=" N GLN B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 408 through 413 removed outlier: 4.329A pdb=" N LEU B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 454 removed outlier: 3.697A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ARG B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 500 Processing helix chain 'B' and resid 504 through 509 removed outlier: 4.287A pdb=" N VAL B 508 " --> pdb=" O LYS B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 531 Processing helix chain 'B' and resid 536 through 551 Processing helix chain 'B' and resid 552 through 557 removed outlier: 3.927A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 599 removed outlier: 3.727A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ARG B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE B 582 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR B 584 " --> pdb=" O PHE B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 639 Processing helix chain 'B' and resid 640 through 642 No H-bonds generated for 'chain 'B' and resid 640 through 642' Processing helix chain 'B' and resid 655 through 684 removed outlier: 3.681A pdb=" N GLU B 684 " --> pdb=" O ALA B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 711 removed outlier: 3.702A pdb=" N ASN B 695 " --> pdb=" O GLN B 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 211 removed outlier: 3.565A pdb=" N ILE C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 223 Processing helix chain 'C' and resid 233 through 237 Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 261 through 269 Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.592A pdb=" N GLN C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 366 Processing helix chain 'C' and resid 394 through 402 Processing helix chain 'C' and resid 408 through 413 removed outlier: 4.329A pdb=" N LEU C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 454 removed outlier: 3.697A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LYS C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ARG C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR C 454 " --> pdb=" O ALA C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 500 Processing helix chain 'C' and resid 504 through 509 removed outlier: 4.287A pdb=" N VAL C 508 " --> pdb=" O LYS C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 531 Processing helix chain 'C' and resid 536 through 551 Processing helix chain 'C' and resid 552 through 557 removed outlier: 3.926A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 599 removed outlier: 3.727A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR C 584 " --> pdb=" O PHE C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 639 Processing helix chain 'C' and resid 640 through 642 No H-bonds generated for 'chain 'C' and resid 640 through 642' Processing helix chain 'C' and resid 655 through 684 removed outlier: 3.681A pdb=" N GLU C 684 " --> pdb=" O ALA C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 711 removed outlier: 3.702A pdb=" N ASN C 695 " --> pdb=" O GLN C 691 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 369 through 374 removed outlier: 5.959A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 369 through 374 removed outlier: 5.959A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 369 through 374 removed outlier: 5.959A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 369 through 374 removed outlier: 5.959A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) 984 hydrogen bonds defined for protein. 2856 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.05 Time building geometry restraints manager: 3.52 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: 8.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 0.510 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 31.350 Find NCS groups from input model: 0.340 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: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.770 ------------------------------------------------------------------------------- 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 aren 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 : 0.618 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: 0.2244 time to fit residues: 77.2032 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 : 0.697 ------------------------------------------------------------------------------- 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 = 56)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.098808 restraints weight = 74207.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.103708 restraints weight = 42960.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.105766 restraints weight = 30769.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.107727 restraints weight = 25234.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.108926 restraints weight = 21812.130| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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 aren 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 : 0.658 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: 0.7614 (mm) cc_final: 0.7405 (tt) REVERT: D 357 ILE cc_start: 0.7622 (mm) cc_final: 0.7413 (tt) REVERT: B 357 ILE cc_start: 0.7624 (mm) cc_final: 0.7411 (tt) REVERT: C 357 ILE cc_start: 0.7623 (mm) cc_final: 0.7409 (tt) outliers start: 9 outliers final: 9 residues processed: 208 average time/residue: 0.2814 time to fit residues: 88.4749 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 : 0.822 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.154999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.115688 restraints weight = 77176.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.113881 restraints weight = 69233.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.116783 restraints weight = 60516.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.117356 restraints weight = 39243.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.119652 restraints weight = 35300.676| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1006 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= 0.127 Angle : 0.470 6.485 24172 Z= 0.258 Chirality : 0.035 0.123 2704 Planarity : 0.003 0.032 2984 Dihedral : 7.967 137.486 2472 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.16 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 aren not related in a simple way. whole: 1.27 (0.19), residues: 2124 helix: 2.37 (0.15), residues: 1296 sheet: -1.09 (0.61), 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 0.00278 (17872) covalent geometry : angle 0.46952 (24172) hydrogen bonds : bond 0.05520 ( 984) hydrogen bonds : angle 4.00939 ( 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 : 0.973 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: 0.7699 (OUTLIER) cc_final: 0.7441 (mp) REVERT: B 268 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7439 (mp) REVERT: C 268 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7434 (mp) outliers start: 15 outliers final: 12 residues processed: 200 average time/residue: 0.2520 time to fit residues: 77.3127 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 : 0.702 ------------------------------------------------------------------------------- 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: 9.9990 chunk 81 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 198 optimal weight: 1.9990 chunk 156 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3855 r_free = 0.3855 target = 0.149684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.110929 restraints weight = 78232.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.114694 restraints weight = 80629.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.116106 restraints weight = 55011.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.117166 restraints weight = 34645.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.121281 restraints weight = 30233.115| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 17872 Z= 0.264 Angle : 0.569 5.549 24172 Z= 0.322 Chirality : 0.039 0.153 2704 Planarity : 0.004 0.031 2984 Dihedral : 9.038 140.670 2472 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 1.65 % Allowed : 10.19 % Favored : 88.16 % 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 aren not related in a simple way. whole: 0.76 (0.19), residues: 2124 helix: 2.10 (0.15), residues: 1244 sheet: -2.05 (0.59), residues: 92 loop : -1.92 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 409 TYR 0.016 0.002 TYR B 453 PHE 0.018 0.002 PHE C 649 TRP 0.004 0.001 TRP D 372 HIS 0.002 0.001 HIS C 358 Details of bonding type rmsd covalent geometry : bond 0.00625 (17872) covalent geometry : angle 0.56943 (24172) hydrogen bonds : bond 0.07785 ( 984) hydrogen bonds : angle 4.50276 ( 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 219 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 188 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 268 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7493 (mp) REVERT: B 268 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7520 (mp) REVERT: B 677 MET cc_start: 0.6689 (ttm) cc_final: 0.6439 (ttm) REVERT: C 268 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7526 (mp) outliers start: 31 outliers final: 19 residues processed: 200 average time/residue: 0.2554 time to fit residues: 78.6337 Evaluate side-chains 211 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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: 2.9990 chunk 61 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 195 optimal weight: 0.7980 chunk 209 optimal weight: 8.9990 chunk 34 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 chunk 190 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.3891 r_free = 0.3891 target = 0.152675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.113739 restraints weight = 77734.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.113042 restraints weight = 74338.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.114662 restraints weight = 70544.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.118997 restraints weight = 40778.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.119285 restraints weight = 30879.780| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 17872 Z= 0.144 Angle : 0.478 5.120 24172 Z= 0.266 Chirality : 0.035 0.120 2704 Planarity : 0.003 0.032 2984 Dihedral : 8.489 133.582 2472 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.65 % Allowed : 11.25 % Favored : 87.10 % 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 aren not related in a simple way. whole: 1.07 (0.19), residues: 2124 helix: 2.39 (0.15), residues: 1244 sheet: -1.91 (0.60), residues: 92 loop : -1.87 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 363 TYR 0.012 0.001 TYR A 565 PHE 0.010 0.001 PHE A 649 TRP 0.004 0.001 TRP D 272 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00317 (17872) covalent geometry : angle 0.47764 (24172) hydrogen bonds : bond 0.06144 ( 984) hydrogen bonds : angle 4.07054 ( 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 227 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 0.758 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: 0.6608 (ttm) cc_final: 0.6399 (ttm) REVERT: D 677 MET cc_start: 0.6593 (ttm) cc_final: 0.6388 (ttm) REVERT: B 677 MET cc_start: 0.6580 (ttm) cc_final: 0.6378 (ttm) outliers start: 31 outliers final: 27 residues processed: 208 average time/residue: 0.2541 time to fit residues: 80.7975 Evaluate side-chains 227 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 593 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 72 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.151343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.112227 restraints weight = 77888.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.112585 restraints weight = 75163.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.114247 restraints weight = 66317.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.116128 restraints weight = 37399.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.117018 restraints weight = 32147.383| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1550 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= 0.185 Angle : 0.504 5.370 24172 Z= 0.282 Chirality : 0.036 0.118 2704 Planarity : 0.003 0.030 2984 Dihedral : 8.528 134.336 2472 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.75 % Allowed : 11.62 % 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 aren not related in a simple way. whole: 0.96 (0.19), residues: 2124 helix: 2.31 (0.15), residues: 1244 sheet: -1.98 (0.59), residues: 92 loop : -1.91 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 363 TYR 0.011 0.001 TYR A 565 PHE 0.013 0.001 PHE A 649 TRP 0.007 0.001 TRP A 272 HIS 0.001 0.000 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00429 (17872) covalent geometry : angle 0.50372 (24172) hydrogen bonds : bond 0.06624 ( 984) hydrogen bonds : angle 4.15608 ( 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: 33 poor density : 204 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 28 residues processed: 220 average time/residue: 0.2306 time to fit residues: 78.5766 Evaluate side-chains 228 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 593 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 124 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 205 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 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: 3.9990 chunk 143 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 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 = 0.3880 r_free = 0.3880 target = 0.151943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.111470 restraints weight = 78178.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.110710 restraints weight = 68940.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.112882 restraints weight = 64801.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.114048 restraints weight = 38924.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.117243 restraints weight = 35022.341| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 17872 Z= 0.172 Angle : 0.497 6.478 24172 Z= 0.277 Chirality : 0.036 0.119 2704 Planarity : 0.003 0.031 2984 Dihedral : 8.333 131.657 2472 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 1.91 % Allowed : 11.31 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.19), residues: 2124 helix: 2.35 (0.15), residues: 1244 sheet: -2.05 (0.59), residues: 92 loop : -1.90 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 363 TYR 0.010 0.001 TYR D 565 PHE 0.012 0.001 PHE D 649 TRP 0.009 0.001 TRP A 272 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00392 (17872) covalent geometry : angle 0.49696 (24172) hydrogen bonds : bond 0.06439 ( 984) hydrogen bonds : angle 4.09825 ( 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 236 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 36 residues processed: 220 average time/residue: 0.2481 time to fit residues: 84.7883 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 : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 593 THR Rotamers are restrained with sigma=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: 1.9990 chunk 123 optimal weight: 8.9990 chunk 133 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 183 optimal weight: 0.5980 chunk 180 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.154310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.114982 restraints weight = 77576.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.113963 restraints weight = 74301.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.116144 restraints weight = 66153.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.117545 restraints weight = 40295.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.118719 restraints weight = 35722.889| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17872 Z= 0.122 Angle : 0.468 7.134 24172 Z= 0.257 Chirality : 0.034 0.118 2704 Planarity : 0.003 0.030 2984 Dihedral : 7.860 125.569 2472 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.70 % Allowed : 11.46 % Favored : 86.84 % 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 aren not related in a simple way. whole: 1.27 (0.19), residues: 2124 helix: 2.58 (0.15), residues: 1244 sheet: -1.98 (0.59), residues: 92 loop : -1.81 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 363 TYR 0.011 0.001 TYR C 565 PHE 0.008 0.001 PHE D 591 TRP 0.011 0.001 TRP A 272 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00266 (17872) covalent geometry : angle 0.46808 (24172) hydrogen bonds : bond 0.05485 ( 984) hydrogen bonds : angle 3.85488 ( 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 231 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 28 residues processed: 215 average time/residue: 0.2298 time to fit residues: 76.7711 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 : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 593 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 124 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 164 optimal weight: 0.5980 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.153272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113938 restraints weight = 77268.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.114434 restraints weight = 73095.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.115979 restraints weight = 65578.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.118207 restraints weight = 36712.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.119315 restraints weight = 31018.507| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17872 Z= 0.143 Angle : 0.483 7.697 24172 Z= 0.266 Chirality : 0.035 0.119 2704 Planarity : 0.003 0.030 2984 Dihedral : 7.796 124.424 2472 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.49 % Allowed : 11.84 % 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 aren not related in a simple way. whole: 1.24 (0.19), residues: 2124 helix: 2.56 (0.15), residues: 1244 sheet: -1.93 (0.59), 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 0.011 0.001 PHE A 649 TRP 0.014 0.001 TRP A 272 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00323 (17872) covalent geometry : angle 0.48277 (24172) hydrogen bonds : bond 0.05817 ( 984) hydrogen bonds : angle 3.91127 ( 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 229 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 0.845 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: 217 average time/residue: 0.2327 time to fit residues: 77.9759 Evaluate side-chains 228 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 593 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 142 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 202 optimal weight: 0.9980 chunk 158 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 = 0.3882 r_free = 0.3882 target = 0.152110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.112567 restraints weight = 77794.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.112302 restraints weight = 72608.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.113633 restraints weight = 74375.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.118989 restraints weight = 41993.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.119131 restraints weight = 28972.798| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17872 Z= 0.172 Angle : 0.507 8.575 24172 Z= 0.281 Chirality : 0.036 0.119 2704 Planarity : 0.003 0.031 2984 Dihedral : 7.787 123.233 2472 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.49 % Allowed : 12.05 % Favored : 86.46 % 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 aren not related in a simple way. whole: 1.09 (0.19), residues: 2124 helix: 2.44 (0.15), residues: 1244 sheet: -2.03 (0.59), residues: 92 loop : -1.89 (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 0.013 0.001 PHE B 649 TRP 0.017 0.001 TRP A 272 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00396 (17872) covalent geometry : angle 0.50705 (24172) hydrogen bonds : bond 0.06317 ( 984) hydrogen bonds : angle 4.03777 ( 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 231 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 203 time to evaluate : 0.629 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: 219 average time/residue: 0.2297 time to fit residues: 77.7650 Evaluate side-chains 232 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 593 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 158 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 6 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 93 optimal weight: 0.0050 chunk 143 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 31 optimal weight: 0.0970 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 ASN B 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.154151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.114617 restraints weight = 75790.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.114863 restraints weight = 65155.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.116559 restraints weight = 64496.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.118227 restraints weight = 37398.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.119696 restraints weight = 33206.266| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1724 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= 0.113 Angle : 0.468 8.434 24172 Z= 0.255 Chirality : 0.034 0.132 2704 Planarity : 0.003 0.031 2984 Dihedral : 7.347 117.807 2472 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.27 % Allowed : 12.42 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.19), residues: 2124 helix: 2.71 (0.15), residues: 1244 sheet: -1.88 (0.60), residues: 92 loop : -1.78 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 575 TYR 0.011 0.001 TYR A 565 PHE 0.007 0.001 PHE D 659 TRP 0.018 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 0.46824 (24172) hydrogen bonds : bond 0.05096 ( 984) hydrogen bonds : angle 3.74465 ( 2856) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3800.81 seconds wall clock time: 65 minutes 42.25 seconds (3942.25 seconds total)