Starting phenix.real_space_refine on Tue Aug 4 23:01:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oef_70397/08_2026/9oef_70397.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oef_70397/08_2026/9oef_70397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oef_70397/08_2026/9oef_70397.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oef_70397/08_2026/9oef_70397.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oef_70397/08_2026/9oef_70397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oef_70397/08_2026/9oef_70397.map" } resolution = 2.69 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= -0.000 sd= 0.028 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 4564 2.51 5 N 1200 2.21 5 O 1348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7148 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 2148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2148 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 16, 'TRANS': 255} Chain breaks: 1 Chain: "H" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain breaks: 1 Chain: "L" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 613 Classifications: {'peptide': 81} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 74} Chain breaks: 3 Restraints were copied for chains: A, J, K Time building chain proxies: 1.63, per 1000 atoms: 0.23 Number of scatterers: 7148 At special positions: 0 Unit cell: (78.85, 130.31, 79.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1348 8.00 N 1200 7.00 C 4564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 338.7 milliseconds 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1656 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 16 sheets defined 3.3% alpha, 53.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'C' and resid 658 through 664 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 41 through 43 No H-bonds generated for 'chain 'H' and resid 41 through 43' Processing helix chain 'A' and resid 658 through 664 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 41 through 43 No H-bonds generated for 'chain 'J' and resid 41 through 43' Processing sheet with id=AA1, first strand: chain 'C' and resid 471 through 476 removed outlier: 6.394A pdb=" N VAL C 466 " --> pdb=" O VAL C 473 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ALA C 475 " --> pdb=" O PHE C 464 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N PHE C 464 " --> pdb=" O ALA C 475 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL C 513 " --> pdb=" O GLY C 524 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY C 524 " --> pdb=" O VAL C 513 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU C 554 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TRP C 531 " --> pdb=" O TYR C 552 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TYR C 552 " --> pdb=" O TRP C 531 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER C 533 " --> pdb=" O LEU C 550 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU C 550 " --> pdb=" O SER C 533 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLU C 535 " --> pdb=" O LEU C 548 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU C 548 " --> pdb=" O GLU C 535 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE C 619 " --> pdb=" O PHE C 482 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL C 489 " --> pdb=" O TRP C 500 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TRP C 500 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THR C 491 " --> pdb=" O SER C 498 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 471 through 476 removed outlier: 6.394A pdb=" N VAL C 466 " --> pdb=" O VAL C 473 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ALA C 475 " --> pdb=" O PHE C 464 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N PHE C 464 " --> pdb=" O ALA C 475 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL C 513 " --> pdb=" O GLY C 524 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY C 524 " --> pdb=" O VAL C 513 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU C 554 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TRP C 531 " --> pdb=" O TYR C 552 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TYR C 552 " --> pdb=" O TRP C 531 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER C 533 " --> pdb=" O LEU C 550 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU C 550 " --> pdb=" O SER C 533 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLU C 535 " --> pdb=" O LEU C 548 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU C 548 " --> pdb=" O GLU C 535 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE C 619 " --> pdb=" O PHE C 482 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP C 671 " --> pdb=" O MET C 425 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 429 through 432 removed outlier: 3.781A pdb=" N PHE C 566 " --> pdb=" O ALA C 608 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 445 through 446 removed outlier: 4.489A pdb=" N GLN C 570 " --> pdb=" O PHE C 597 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR C 576 " --> pdb=" O LYS C 591 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LYS C 591 " --> pdb=" O TYR C 576 " (cutoff:3.500A) removed outlier: 12.091A pdb=" N GLU C 578 " --> pdb=" O ILE C 589 " (cutoff:3.500A) removed outlier: 10.566A pdb=" N ILE C 589 " --> pdb=" O GLU C 578 " (cutoff:3.500A) removed outlier: 10.567A pdb=" N ILE A 589 " --> pdb=" O GLU A 578 " (cutoff:3.500A) removed outlier: 12.092A pdb=" N GLU A 578 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LYS A 591 " --> pdb=" O TYR A 576 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR A 576 " --> pdb=" O LYS A 591 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLN A 570 " --> pdb=" O PHE A 597 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 646 through 647 Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA7, first strand: chain 'H' and resid 57 through 58 removed outlier: 5.554A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 6 removed outlier: 4.229A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 53 through 54 removed outlier: 5.892A pdb=" N GLN L 37 " --> pdb=" O PRO L 46 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 471 through 476 removed outlier: 6.395A pdb=" N VAL A 466 " --> pdb=" O VAL A 473 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ALA A 475 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N PHE A 464 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL A 513 " --> pdb=" O GLY A 524 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY A 524 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU A 554 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TRP A 531 " --> pdb=" O TYR A 552 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TYR A 552 " --> pdb=" O TRP A 531 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER A 533 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU A 550 " --> pdb=" O SER A 533 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLU A 535 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU A 548 " --> pdb=" O GLU A 535 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A 619 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL A 489 " --> pdb=" O TRP A 500 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TRP A 500 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N THR A 491 " --> pdb=" O SER A 498 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 471 through 476 removed outlier: 6.395A pdb=" N VAL A 466 " --> pdb=" O VAL A 473 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ALA A 475 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N PHE A 464 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL A 513 " --> pdb=" O GLY A 524 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY A 524 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU A 554 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TRP A 531 " --> pdb=" O TYR A 552 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TYR A 552 " --> pdb=" O TRP A 531 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER A 533 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU A 550 " --> pdb=" O SER A 533 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLU A 535 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU A 548 " --> pdb=" O GLU A 535 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A 619 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP A 671 " --> pdb=" O MET A 425 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 429 through 432 removed outlier: 3.781A pdb=" N PHE A 566 " --> pdb=" O ALA A 608 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 3 through 5 Processing sheet with id=AB5, first strand: chain 'J' and resid 57 through 58 removed outlier: 5.555A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 4 through 6 removed outlier: 4.230A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 53 through 54 removed outlier: 5.891A pdb=" N GLN K 37 " --> pdb=" O PRO K 46 " (cutoff:3.500A) 280 hydrogen bonds defined for protein. 714 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.04 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2246 1.34 - 1.46: 1986 1.46 - 1.58: 3060 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 7352 Sorted by residual: bond pdb=" C HIS A 451 " pdb=" O HIS A 451 " ideal model delta sigma weight residual 1.248 1.236 0.012 1.26e-02 6.30e+03 9.25e-01 bond pdb=" C HIS C 451 " pdb=" O HIS C 451 " ideal model delta sigma weight residual 1.248 1.237 0.012 1.26e-02 6.30e+03 8.39e-01 bond pdb=" C VAL H 63 " pdb=" O VAL H 63 " ideal model delta sigma weight residual 1.231 1.242 -0.011 1.51e-02 4.39e+03 4.98e-01 bond pdb=" CA PRO C 452 " pdb=" C PRO C 452 " ideal model delta sigma weight residual 1.528 1.519 0.008 1.20e-02 6.94e+03 4.57e-01 bond pdb=" CA PRO A 452 " pdb=" C PRO A 452 " ideal model delta sigma weight residual 1.528 1.520 0.008 1.20e-02 6.94e+03 4.41e-01 ... (remaining 7347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 9595 1.21 - 2.42: 341 2.42 - 3.63: 63 3.63 - 4.84: 5 4.84 - 6.05: 2 Bond angle restraints: 10006 Sorted by residual: angle pdb=" N GLY C 413 " pdb=" CA GLY C 413 " pdb=" C GLY C 413 " ideal model delta sigma weight residual 112.29 115.36 -3.07 1.12e+00 7.97e-01 7.50e+00 angle pdb=" N GLY A 413 " pdb=" CA GLY A 413 " pdb=" C GLY A 413 " ideal model delta sigma weight residual 112.29 115.31 -3.02 1.12e+00 7.97e-01 7.28e+00 angle pdb=" N GLY C 626 " pdb=" CA GLY C 626 " pdb=" C GLY C 626 " ideal model delta sigma weight residual 110.38 113.35 -2.97 1.42e+00 4.96e-01 4.37e+00 angle pdb=" N GLY A 626 " pdb=" CA GLY A 626 " pdb=" C GLY A 626 " ideal model delta sigma weight residual 110.38 113.33 -2.95 1.42e+00 4.96e-01 4.30e+00 angle pdb=" CA GLY C 626 " pdb=" C GLY C 626 " pdb=" N ARG C 627 " ideal model delta sigma weight residual 114.82 117.34 -2.52 1.23e+00 6.61e-01 4.19e+00 ... (remaining 10001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.22: 3968 13.22 - 26.44: 210 26.44 - 39.66: 40 39.66 - 52.88: 12 52.88 - 66.10: 4 Dihedral angle restraints: 4234 sinusoidal: 1640 harmonic: 2594 Sorted by residual: dihedral pdb=" CA ALA H 88 " pdb=" C ALA H 88 " pdb=" N ILE H 89 " pdb=" CA ILE H 89 " ideal model delta harmonic sigma weight residual -180.00 -160.74 -19.26 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ALA J 88 " pdb=" C ALA J 88 " pdb=" N ILE J 89 " pdb=" CA ILE J 89 " ideal model delta harmonic sigma weight residual -180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA LEU A 467 " pdb=" C LEU A 467 " pdb=" N GLU A 468 " pdb=" CA GLU A 468 " ideal model delta harmonic sigma weight residual 180.00 162.44 17.56 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 4231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 701 0.030 - 0.061: 242 0.061 - 0.091: 74 0.091 - 0.122: 41 0.122 - 0.152: 12 Chirality restraints: 1070 Sorted by residual: chirality pdb=" CA ILE H 37 " pdb=" N ILE H 37 " pdb=" C ILE H 37 " pdb=" CB ILE H 37 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" CA ILE J 37 " pdb=" N ILE J 37 " pdb=" C ILE J 37 " pdb=" CB ILE J 37 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA ILE A 622 " pdb=" N ILE A 622 " pdb=" C ILE A 622 " pdb=" CB ILE A 622 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 1067 not shown) Planarity restraints: 1266 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 572 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO C 573 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 573 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 573 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 542 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO A 543 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 543 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 543 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 572 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO A 573 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 573 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 573 " -0.019 5.00e-02 4.00e+02 ... (remaining 1263 not shown) Histogram of nonbonded interaction distances: 2.62 - 3.08: 4510 3.08 - 3.53: 6784 3.53 - 3.99: 11649 3.99 - 4.44: 14155 4.44 - 4.90: 22683 Nonbonded interactions: 59781 Sorted by model distance: nonbonded pdb=" N THR H 87 " pdb=" O THR H 87 " model vdw 2.624 2.496 nonbonded pdb=" N THR J 87 " pdb=" O THR J 87 " model vdw 2.625 2.496 nonbonded pdb=" N VAL C 473 " pdb=" N GLY C 474 " model vdw 2.630 2.560 nonbonded pdb=" N VAL A 473 " pdb=" N GLY A 474 " model vdw 2.631 2.560 nonbonded pdb=" N THR A 581 " pdb=" O THR A 581 " model vdw 2.639 2.496 ... (remaining 59776 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: 0.01 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'A' } ncs_group { reference = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.670 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:7.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 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 : 0.002 0.015 7354 Z= 0.119 Angle : 0.540 6.047 10010 Z= 0.313 Chirality : 0.040 0.152 1070 Planarity : 0.003 0.035 1266 Dihedral : 8.838 66.101 2572 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.03 % Allowed : 4.13 % Favored : 94.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.27), residues: 876 helix: -0.33 (1.75), residues: 12 sheet: 0.72 (0.28), residues: 306 loop : -0.20 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 71 TYR 0.009 0.001 TYR C 552 PHE 0.007 0.001 PHE C 420 TRP 0.008 0.001 TRP C 490 HIS 0.002 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.12 ( 7352) covalent geometry : angle 0.53940 / 0.31 (10006) SS BOND : bond 0.00560 / 0.33 ( 2) SS BOND : angle 0.96846 / 0.55 ( 4) hydrogen bonds : bond 0.12151 / 8.81 ( 223) hydrogen bonds : angle 6.53589 / 4.49 ( 714) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 0.290 Fit side-chains REVERT: C 424 ARG cc_start: 0.7628 (mtm180) cc_final: 0.6865 (mtt-85) REVERT: C 541 GLU cc_start: 0.7335 (pt0) cc_final: 0.6659 (tm-30) REVERT: C 631 ASP cc_start: 0.8078 (t0) cc_final: 0.7803 (t0) REVERT: C 650 GLN cc_start: 0.7901 (pt0) cc_final: 0.7007 (mm-40) REVERT: H 58 TYR cc_start: 0.5861 (m-80) cc_final: 0.5570 (m-80) REVERT: A 424 ARG cc_start: 0.7643 (mtm180) cc_final: 0.6871 (mtt-85) REVERT: A 541 GLU cc_start: 0.7348 (pt0) cc_final: 0.6760 (tm-30) REVERT: A 631 ASP cc_start: 0.8093 (t0) cc_final: 0.7771 (t0) REVERT: A 650 GLN cc_start: 0.7874 (pt0) cc_final: 0.7007 (mm-40) outliers start: 8 outliers final: 4 residues processed: 146 average time/residue: 0.6222 time to fit residues: 94.9411 Evaluate side-chains 108 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 555 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.0980 chunk 74 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 495 GLN ** C 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 90 GLN A 495 GLN ** A 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN K 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.183389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.149270 restraints weight = 7349.099| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.25 r_work: 0.3812 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3687 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 7354 Z= 0.260 Angle : 0.668 9.149 10010 Z= 0.349 Chirality : 0.046 0.149 1070 Planarity : 0.005 0.040 1266 Dihedral : 6.208 54.733 978 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.52 % Allowed : 8.27 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.27), residues: 876 helix: -1.54 (1.42), residues: 12 sheet: 0.46 (0.27), residues: 310 loop : -0.57 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 615 TYR 0.017 0.003 TYR C 552 PHE 0.022 0.002 PHE K 98 TRP 0.023 0.003 TRP L 91 HIS 0.004 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00613 / 0.26 ( 7352) covalent geometry : angle 0.66740 / 0.35 (10006) SS BOND : bond 0.00716 / 0.43 ( 2) SS BOND : angle 1.20503 / 0.72 ( 4) hydrogen bonds : bond 0.04089 / 2.90 ( 223) hydrogen bonds : angle 5.79486 / 4.04 ( 714) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 0.167 Fit side-chains REVERT: C 424 ARG cc_start: 0.7571 (mtm180) cc_final: 0.6559 (mtt-85) REVERT: C 534 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8833 (tt0) REVERT: C 541 GLU cc_start: 0.7233 (pt0) cc_final: 0.6379 (tm-30) REVERT: C 631 ASP cc_start: 0.8121 (t0) cc_final: 0.7783 (t0) REVERT: C 641 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: C 650 GLN cc_start: 0.7744 (pt0) cc_final: 0.6701 (mm-40) REVERT: H 38 ARG cc_start: 0.6034 (OUTLIER) cc_final: 0.5393 (ptp90) REVERT: L 72 SER cc_start: 0.7631 (p) cc_final: 0.7411 (m) REVERT: A 424 ARG cc_start: 0.7553 (mtm180) cc_final: 0.6536 (mtt-85) REVERT: A 534 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8819 (tt0) REVERT: A 541 GLU cc_start: 0.7191 (pt0) cc_final: 0.6359 (tm-30) REVERT: A 631 ASP cc_start: 0.8143 (t0) cc_final: 0.7804 (t0) REVERT: A 641 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: A 650 GLN cc_start: 0.7752 (pt0) cc_final: 0.6714 (mm-40) REVERT: J 38 ARG cc_start: 0.5992 (OUTLIER) cc_final: 0.5324 (ptt90) outliers start: 35 outliers final: 14 residues processed: 126 average time/residue: 0.5456 time to fit residues: 72.3369 Evaluate side-chains 120 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 89 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 85 optimal weight: 0.0050 chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 433 GLN C 470 ASN C 628 HIS L 6 GLN L 90 GLN A 433 GLN A 470 ASN A 628 HIS K 6 GLN K 90 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.188400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.154264 restraints weight = 7266.986| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.29 r_work: 0.3867 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3742 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7354 Z= 0.105 Angle : 0.522 7.278 10010 Z= 0.272 Chirality : 0.041 0.142 1070 Planarity : 0.004 0.036 1266 Dihedral : 5.117 46.654 974 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.84 % Allowed : 12.66 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.27), residues: 876 helix: -1.24 (1.47), residues: 12 sheet: 0.57 (0.28), residues: 300 loop : -0.57 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 61 TYR 0.011 0.001 TYR K 49 PHE 0.013 0.001 PHE K 98 TRP 0.014 0.001 TRP L 91 HIS 0.002 0.001 HIS C 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 7352) covalent geometry : angle 0.52180 / 0.27 (10006) SS BOND : bond 0.00624 / 0.38 ( 2) SS BOND : angle 1.21628 / 0.75 ( 4) hydrogen bonds : bond 0.03206 / 2.24 ( 223) hydrogen bonds : angle 5.32407 / 3.68 ( 714) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.254 Fit side-chains REVERT: C 424 ARG cc_start: 0.7453 (mtm180) cc_final: 0.6421 (mtt-85) REVERT: C 541 GLU cc_start: 0.7154 (pt0) cc_final: 0.6299 (tm-30) REVERT: C 631 ASP cc_start: 0.8151 (t0) cc_final: 0.7715 (t0) REVERT: C 650 GLN cc_start: 0.7701 (pt0) cc_final: 0.6622 (mm-40) REVERT: H 94 ARG cc_start: 0.7947 (ttp-170) cc_final: 0.7731 (ttp-170) REVERT: L 72 SER cc_start: 0.7520 (p) cc_final: 0.7319 (m) REVERT: A 424 ARG cc_start: 0.7443 (mtm180) cc_final: 0.6407 (mtt-85) REVERT: A 535 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6814 (pm20) REVERT: A 541 GLU cc_start: 0.7187 (pt0) cc_final: 0.6355 (tm-30) REVERT: A 631 ASP cc_start: 0.8116 (t0) cc_final: 0.7726 (t0) REVERT: A 650 GLN cc_start: 0.7704 (pt0) cc_final: 0.6623 (mm-40) REVERT: J 38 ARG cc_start: 0.5900 (OUTLIER) cc_final: 0.5362 (ptp90) REVERT: J 58 TYR cc_start: 0.5080 (m-80) cc_final: 0.4621 (m-80) REVERT: J 94 ARG cc_start: 0.7955 (ttp-170) cc_final: 0.7729 (ttp-170) outliers start: 22 outliers final: 7 residues processed: 122 average time/residue: 0.6022 time to fit residues: 77.1032 Evaluate side-chains 115 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain K residue 89 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 17 optimal weight: 0.3980 chunk 37 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 49 optimal weight: 0.1980 chunk 3 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 66 optimal weight: 0.0970 chunk 4 optimal weight: 0.0870 chunk 75 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 90 GLN K 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.191178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.156562 restraints weight = 7336.258| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.33 r_work: 0.3891 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3766 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7354 Z= 0.090 Angle : 0.500 6.771 10010 Z= 0.260 Chirality : 0.040 0.138 1070 Planarity : 0.004 0.035 1266 Dihedral : 4.820 43.717 974 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.58 % Allowed : 13.31 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.27), residues: 876 helix: -0.92 (1.55), residues: 12 sheet: 0.62 (0.28), residues: 300 loop : -0.59 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 61 TYR 0.011 0.001 TYR K 87 PHE 0.010 0.001 PHE K 98 TRP 0.012 0.001 TRP L 91 HIS 0.002 0.001 HIS C 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 ( 7352) covalent geometry : angle 0.49973 / 0.26 (10006) SS BOND : bond 0.00601 / 0.36 ( 2) SS BOND : angle 1.08874 / 0.66 ( 4) hydrogen bonds : bond 0.02978 / 2.09 ( 223) hydrogen bonds : angle 5.06260 / 3.51 ( 714) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.233 Fit side-chains REVERT: C 424 ARG cc_start: 0.7397 (mtm180) cc_final: 0.6359 (mtt-85) REVERT: C 541 GLU cc_start: 0.7164 (pt0) cc_final: 0.6321 (tm-30) REVERT: C 631 ASP cc_start: 0.8100 (t0) cc_final: 0.7787 (t0) REVERT: C 650 GLN cc_start: 0.7635 (pt0) cc_final: 0.6596 (mm-40) REVERT: H 58 TYR cc_start: 0.5072 (m-80) cc_final: 0.4567 (m-80) REVERT: H 64 LYS cc_start: 0.7421 (tttm) cc_final: 0.7158 (mtpt) REVERT: H 94 ARG cc_start: 0.7905 (ttp-170) cc_final: 0.7666 (ttp-170) REVERT: A 424 ARG cc_start: 0.7404 (mtm180) cc_final: 0.6363 (mtt-85) REVERT: A 541 GLU cc_start: 0.7166 (pt0) cc_final: 0.6337 (tm-30) REVERT: A 631 ASP cc_start: 0.8161 (t0) cc_final: 0.7886 (t0) REVERT: A 650 GLN cc_start: 0.7661 (pt0) cc_final: 0.6639 (mm-40) REVERT: J 58 TYR cc_start: 0.5127 (m-80) cc_final: 0.4578 (m-80) REVERT: J 64 LYS cc_start: 0.7407 (tttm) cc_final: 0.7193 (mtpt) REVERT: J 94 ARG cc_start: 0.7928 (ttp-170) cc_final: 0.7684 (ttp-170) outliers start: 20 outliers final: 11 residues processed: 122 average time/residue: 0.5962 time to fit residues: 76.5837 Evaluate side-chains 117 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 89 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 55 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 4 optimal weight: 0.2980 chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 90 GLN ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.186233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.151680 restraints weight = 7407.580| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.32 r_work: 0.3839 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3716 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7354 Z= 0.166 Angle : 0.574 7.990 10010 Z= 0.297 Chirality : 0.043 0.142 1070 Planarity : 0.004 0.036 1266 Dihedral : 5.187 46.683 974 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.75 % Allowed : 13.31 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.27), residues: 876 helix: -1.39 (1.43), residues: 12 sheet: 0.50 (0.28), residues: 314 loop : -0.73 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 615 TYR 0.013 0.002 TYR C 552 PHE 0.016 0.002 PHE L 98 TRP 0.016 0.002 TRP L 91 HIS 0.004 0.001 HIS C 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 7352) covalent geometry : angle 0.57375 / 0.30 (10006) SS BOND : bond 0.00530 / 0.32 ( 2) SS BOND : angle 1.26448 / 0.77 ( 4) hydrogen bonds : bond 0.03410 / 2.39 ( 223) hydrogen bonds : angle 5.31758 / 3.70 ( 714) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.262 Fit side-chains REVERT: C 424 ARG cc_start: 0.7467 (mtm180) cc_final: 0.6421 (mtt-85) REVERT: C 541 GLU cc_start: 0.7185 (pt0) cc_final: 0.6360 (tm-30) REVERT: C 631 ASP cc_start: 0.8162 (t0) cc_final: 0.7793 (t0) REVERT: C 641 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7410 (mp0) REVERT: C 650 GLN cc_start: 0.7708 (pt0) cc_final: 0.6687 (mm-40) REVERT: H 58 TYR cc_start: 0.5094 (m-80) cc_final: 0.4621 (m-80) REVERT: H 64 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7131 (mtpt) REVERT: H 94 ARG cc_start: 0.7929 (ttp-170) cc_final: 0.7683 (ttp-170) REVERT: A 424 ARG cc_start: 0.7469 (mtm180) cc_final: 0.6417 (mtt-85) REVERT: A 541 GLU cc_start: 0.7219 (pt0) cc_final: 0.6366 (tm-30) REVERT: A 631 ASP cc_start: 0.8190 (t0) cc_final: 0.7841 (t0) REVERT: A 641 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: A 650 GLN cc_start: 0.7694 (pt0) cc_final: 0.6677 (mm-40) REVERT: J 38 ARG cc_start: 0.6063 (OUTLIER) cc_final: 0.5615 (ptp90) REVERT: J 58 TYR cc_start: 0.5187 (m-80) cc_final: 0.4673 (m-80) REVERT: J 64 LYS cc_start: 0.7525 (tttm) cc_final: 0.7302 (mtpt) REVERT: J 94 ARG cc_start: 0.7963 (ttp-170) cc_final: 0.7736 (ttp-170) outliers start: 29 outliers final: 13 residues processed: 124 average time/residue: 0.6339 time to fit residues: 82.4364 Evaluate side-chains 118 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 89 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 34 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 chunk 4 optimal weight: 0.0270 chunk 81 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 40 optimal weight: 0.0370 chunk 73 optimal weight: 6.9990 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 90 GLN ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.190067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.155293 restraints weight = 7375.615| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 2.35 r_work: 0.3883 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3759 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7354 Z= 0.099 Angle : 0.515 6.772 10010 Z= 0.268 Chirality : 0.041 0.140 1070 Planarity : 0.004 0.034 1266 Dihedral : 4.876 45.004 974 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.33 % Allowed : 15.76 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.27), residues: 876 helix: -0.95 (1.55), residues: 12 sheet: 0.69 (0.29), residues: 296 loop : -0.70 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 61 TYR 0.013 0.001 TYR K 49 PHE 0.011 0.001 PHE K 98 TRP 0.015 0.001 TRP L 91 HIS 0.002 0.001 HIS C 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 ( 7352) covalent geometry : angle 0.51478 / 0.27 (10006) SS BOND : bond 0.00598 / 0.36 ( 2) SS BOND : angle 1.21684 / 0.75 ( 4) hydrogen bonds : bond 0.03005 / 2.10 ( 223) hydrogen bonds : angle 5.01642 / 3.47 ( 714) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.175 Fit side-chains REVERT: C 424 ARG cc_start: 0.7405 (mtm180) cc_final: 0.6350 (mtt-85) REVERT: C 541 GLU cc_start: 0.7170 (pt0) cc_final: 0.6342 (tm-30) REVERT: C 631 ASP cc_start: 0.8171 (t0) cc_final: 0.7911 (t0) REVERT: C 650 GLN cc_start: 0.7651 (pt0) cc_final: 0.6661 (mm-40) REVERT: H 58 TYR cc_start: 0.5147 (m-80) cc_final: 0.4595 (m-80) REVERT: H 64 LYS cc_start: 0.7555 (tttm) cc_final: 0.7206 (mtpt) REVERT: H 94 ARG cc_start: 0.7947 (ttp-170) cc_final: 0.7682 (ttp-170) REVERT: A 424 ARG cc_start: 0.7406 (mtm180) cc_final: 0.6342 (mtt-85) REVERT: A 541 GLU cc_start: 0.7158 (pt0) cc_final: 0.6327 (tm-30) REVERT: A 631 ASP cc_start: 0.8185 (t0) cc_final: 0.7866 (t0) REVERT: A 650 GLN cc_start: 0.7640 (pt0) cc_final: 0.6630 (mm-40) REVERT: J 38 ARG cc_start: 0.6038 (OUTLIER) cc_final: 0.5488 (ptp90) REVERT: J 58 TYR cc_start: 0.5251 (m-80) cc_final: 0.4640 (m-80) REVERT: J 64 LYS cc_start: 0.7489 (tttm) cc_final: 0.7281 (mtpt) REVERT: J 94 ARG cc_start: 0.7962 (ttp-170) cc_final: 0.7721 (ttp-170) outliers start: 18 outliers final: 12 residues processed: 116 average time/residue: 0.5225 time to fit residues: 63.6881 Evaluate side-chains 117 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 89 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 11 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 83 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN K 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.182244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.147479 restraints weight = 7427.763| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.36 r_work: 0.3796 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3671 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 7354 Z= 0.255 Angle : 0.665 9.716 10010 Z= 0.342 Chirality : 0.046 0.149 1070 Planarity : 0.005 0.040 1266 Dihedral : 5.554 48.362 974 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.88 % Allowed : 14.34 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.27), residues: 876 helix: -1.77 (1.33), residues: 12 sheet: 0.25 (0.28), residues: 312 loop : -0.88 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 61 TYR 0.016 0.003 TYR A 552 PHE 0.023 0.002 PHE L 98 TRP 0.022 0.003 TRP L 91 HIS 0.006 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.25 ( 7352) covalent geometry : angle 0.66420 / 0.34 (10006) SS BOND : bond 0.00559 / 0.34 ( 2) SS BOND : angle 1.60706 / 0.99 ( 4) hydrogen bonds : bond 0.03880 / 2.72 ( 223) hydrogen bonds : angle 5.58935 / 3.90 ( 714) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.268 Fit side-chains REVERT: C 424 ARG cc_start: 0.7528 (mtm180) cc_final: 0.6376 (mtt-85) REVERT: C 483 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7295 (mm-40) REVERT: C 541 GLU cc_start: 0.7204 (pt0) cc_final: 0.6299 (tm-30) REVERT: C 631 ASP cc_start: 0.8199 (t0) cc_final: 0.7890 (t0) REVERT: C 641 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: H 58 TYR cc_start: 0.5243 (m-80) cc_final: 0.4716 (m-80) REVERT: H 64 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7347 (mttt) REVERT: H 94 ARG cc_start: 0.7939 (ttp-170) cc_final: 0.7700 (ttp-170) REVERT: A 424 ARG cc_start: 0.7518 (mtm180) cc_final: 0.6357 (mtt-85) REVERT: A 483 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7304 (mm-40) REVERT: A 541 GLU cc_start: 0.7235 (pt0) cc_final: 0.6316 (tm-30) REVERT: A 631 ASP cc_start: 0.8231 (t0) cc_final: 0.7929 (t0) REVERT: A 641 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7499 (mp0) REVERT: J 38 ARG cc_start: 0.6211 (OUTLIER) cc_final: 0.5695 (ptp90) REVERT: J 58 TYR cc_start: 0.5347 (m-80) cc_final: 0.4794 (m-80) REVERT: J 64 LYS cc_start: 0.7617 (tttm) cc_final: 0.7334 (mtpt) REVERT: J 94 ARG cc_start: 0.7960 (ttp-170) cc_final: 0.7713 (ttp-170) outliers start: 30 outliers final: 12 residues processed: 112 average time/residue: 0.6264 time to fit residues: 73.5700 Evaluate side-chains 110 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 483 GLN Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 89 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 24 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 89 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.186535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.152004 restraints weight = 7429.097| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.33 r_work: 0.3847 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7354 Z= 0.121 Angle : 0.553 7.911 10010 Z= 0.286 Chirality : 0.042 0.139 1070 Planarity : 0.004 0.039 1266 Dihedral : 5.162 45.656 974 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.97 % Allowed : 15.89 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.27), residues: 876 helix: -1.16 (1.51), residues: 12 sheet: 0.43 (0.28), residues: 310 loop : -0.84 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 61 TYR 0.014 0.001 TYR K 49 PHE 0.013 0.001 PHE K 98 TRP 0.018 0.001 TRP K 91 HIS 0.003 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 7352) covalent geometry : angle 0.55259 / 0.29 (10006) SS BOND : bond 0.00666 / 0.40 ( 2) SS BOND : angle 1.47177 / 0.93 ( 4) hydrogen bonds : bond 0.03232 / 2.26 ( 223) hydrogen bonds : angle 5.25029 / 3.63 ( 714) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.237 Fit side-chains REVERT: C 424 ARG cc_start: 0.7434 (mtm180) cc_final: 0.6357 (mtt-85) REVERT: C 483 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7315 (mm-40) REVERT: C 541 GLU cc_start: 0.7172 (pt0) cc_final: 0.6268 (tm-30) REVERT: C 631 ASP cc_start: 0.8193 (t0) cc_final: 0.7773 (t0) REVERT: C 650 GLN cc_start: 0.7672 (pt0) cc_final: 0.6641 (mm-40) REVERT: H 58 TYR cc_start: 0.5243 (m-80) cc_final: 0.4694 (m-80) REVERT: H 64 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7306 (mtpt) REVERT: H 94 ARG cc_start: 0.7942 (ttp-170) cc_final: 0.7684 (ttp-170) REVERT: A 424 ARG cc_start: 0.7436 (mtm180) cc_final: 0.6346 (mtt-85) REVERT: A 483 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7312 (mm-40) REVERT: A 541 GLU cc_start: 0.7199 (pt0) cc_final: 0.6286 (tm-30) REVERT: A 631 ASP cc_start: 0.8219 (t0) cc_final: 0.7800 (t0) REVERT: A 650 GLN cc_start: 0.7622 (pt0) cc_final: 0.6590 (mm-40) REVERT: J 38 ARG cc_start: 0.6169 (OUTLIER) cc_final: 0.5700 (ptp90) REVERT: J 58 TYR cc_start: 0.5267 (m-80) cc_final: 0.4663 (m-80) REVERT: J 94 ARG cc_start: 0.7936 (ttp-170) cc_final: 0.7684 (ttp-170) outliers start: 23 outliers final: 12 residues processed: 112 average time/residue: 0.5209 time to fit residues: 61.3202 Evaluate side-chains 112 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 483 GLN Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 89 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 13 optimal weight: 0.0270 chunk 3 optimal weight: 0.0770 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.186187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.151635 restraints weight = 7374.729| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.34 r_work: 0.3845 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3721 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7354 Z= 0.142 Angle : 0.569 8.053 10010 Z= 0.293 Chirality : 0.042 0.144 1070 Planarity : 0.004 0.039 1266 Dihedral : 5.177 45.815 974 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.84 % Allowed : 15.63 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.27), residues: 876 helix: -1.25 (1.51), residues: 12 sheet: 0.37 (0.28), residues: 310 loop : -0.84 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 615 TYR 0.014 0.002 TYR K 49 PHE 0.014 0.001 PHE K 98 TRP 0.017 0.002 TRP K 91 HIS 0.003 0.001 HIS C 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 7352) covalent geometry : angle 0.56814 / 0.29 (10006) SS BOND : bond 0.00636 / 0.38 ( 2) SS BOND : angle 1.49313 / 0.94 ( 4) hydrogen bonds : bond 0.03293 / 2.31 ( 223) hydrogen bonds : angle 5.24490 / 3.64 ( 714) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.162 Fit side-chains REVERT: C 424 ARG cc_start: 0.7434 (mtm180) cc_final: 0.6352 (mtt-85) REVERT: C 483 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7293 (mm-40) REVERT: C 631 ASP cc_start: 0.8215 (t0) cc_final: 0.7811 (t0) REVERT: C 650 GLN cc_start: 0.7639 (pt0) cc_final: 0.6639 (mm-40) REVERT: H 58 TYR cc_start: 0.5223 (m-80) cc_final: 0.4673 (m-80) REVERT: H 64 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7327 (mtpt) REVERT: H 94 ARG cc_start: 0.7939 (ttp-170) cc_final: 0.7676 (ttp-170) REVERT: A 424 ARG cc_start: 0.7433 (mtm180) cc_final: 0.6346 (mtt-85) REVERT: A 483 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7292 (mm-40) REVERT: A 534 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8469 (mt-10) REVERT: A 541 GLU cc_start: 0.7207 (pt0) cc_final: 0.6280 (tm-30) REVERT: A 631 ASP cc_start: 0.8236 (t0) cc_final: 0.7835 (t0) REVERT: A 650 GLN cc_start: 0.7621 (pt0) cc_final: 0.6614 (mm-40) REVERT: J 38 ARG cc_start: 0.6128 (OUTLIER) cc_final: 0.5628 (ptp90) REVERT: J 58 TYR cc_start: 0.5258 (m-80) cc_final: 0.4657 (m-80) REVERT: J 94 ARG cc_start: 0.7931 (ttp-170) cc_final: 0.7673 (ttp-170) outliers start: 22 outliers final: 12 residues processed: 108 average time/residue: 0.4693 time to fit residues: 53.4389 Evaluate side-chains 113 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 483 GLN Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 77 optimal weight: 0.0770 chunk 68 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 71 optimal weight: 0.0980 chunk 86 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 69 optimal weight: 0.0060 chunk 20 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.3554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 90 GLN K 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.191746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.157163 restraints weight = 7355.257| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.38 r_work: 0.3912 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3788 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7354 Z= 0.092 Angle : 0.513 6.836 10010 Z= 0.267 Chirality : 0.041 0.140 1070 Planarity : 0.004 0.036 1266 Dihedral : 4.852 44.635 974 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.58 % Allowed : 16.15 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.27), residues: 876 helix: -0.73 (1.65), residues: 12 sheet: 0.57 (0.29), residues: 296 loop : -0.76 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 615 TYR 0.013 0.001 TYR K 49 PHE 0.008 0.001 PHE J 29 TRP 0.018 0.001 TRP K 91 HIS 0.002 0.001 HIS A 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 ( 7352) covalent geometry : angle 0.51249 / 0.27 (10006) SS BOND : bond 0.00602 / 0.36 ( 2) SS BOND : angle 1.24991 / 0.79 ( 4) hydrogen bonds : bond 0.02994 / 2.07 ( 223) hydrogen bonds : angle 4.94089 / 3.42 ( 714) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.156 Fit side-chains REVERT: C 424 ARG cc_start: 0.7359 (mtm180) cc_final: 0.6276 (mtt-85) REVERT: C 483 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7259 (mm-40) REVERT: C 541 GLU cc_start: 0.7171 (pt0) cc_final: 0.6226 (tm-30) REVERT: C 631 ASP cc_start: 0.8196 (t0) cc_final: 0.7820 (t0) REVERT: C 650 GLN cc_start: 0.7608 (pt0) cc_final: 0.6614 (mm-40) REVERT: H 58 TYR cc_start: 0.5251 (m-80) cc_final: 0.4653 (m-80) REVERT: H 64 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7308 (mtpt) REVERT: H 94 ARG cc_start: 0.7954 (ttp-170) cc_final: 0.7675 (ttp-170) REVERT: A 424 ARG cc_start: 0.7389 (mtm180) cc_final: 0.6277 (mtt-85) REVERT: A 483 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7197 (mm-40) REVERT: A 534 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8435 (mt-10) REVERT: A 541 GLU cc_start: 0.7187 (pt0) cc_final: 0.6236 (tm-30) REVERT: A 631 ASP cc_start: 0.8216 (t0) cc_final: 0.7904 (t0) REVERT: A 641 GLU cc_start: 0.8406 (mp0) cc_final: 0.8156 (mp0) REVERT: A 650 GLN cc_start: 0.7595 (pt0) cc_final: 0.6606 (mm-40) REVERT: J 38 ARG cc_start: 0.6051 (OUTLIER) cc_final: 0.5545 (ptp90) REVERT: J 46 GLU cc_start: 0.6473 (tt0) cc_final: 0.6210 (tt0) REVERT: J 58 TYR cc_start: 0.5308 (m-80) cc_final: 0.4674 (m-80) REVERT: J 94 ARG cc_start: 0.7970 (ttp-170) cc_final: 0.7709 (ttp-170) outliers start: 20 outliers final: 10 residues processed: 112 average time/residue: 0.4906 time to fit residues: 57.8427 Evaluate side-chains 112 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 483 GLN Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 90 GLN K 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.187856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.153406 restraints weight = 7362.287| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.33 r_work: 0.3871 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3746 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7354 Z= 0.130 Angle : 0.547 7.432 10010 Z= 0.283 Chirality : 0.042 0.141 1070 Planarity : 0.004 0.035 1266 Dihedral : 4.991 45.875 974 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.71 % Allowed : 15.76 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.27), residues: 876 helix: -1.47 (1.41), residues: 14 sheet: 0.56 (0.29), residues: 306 loop : -0.77 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 615 TYR 0.014 0.002 TYR K 49 PHE 0.011 0.001 PHE K 98 TRP 0.016 0.001 TRP L 91 HIS 0.003 0.001 HIS C 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 7352) covalent geometry : angle 0.54677 / 0.28 (10006) SS BOND : bond 0.00603 / 0.36 ( 2) SS BOND : angle 1.38092 / 0.88 ( 4) hydrogen bonds : bond 0.03208 / 2.22 ( 223) hydrogen bonds : angle 5.03275 / 3.51 ( 714) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2640.15 seconds wall clock time: 45 minutes 33.39 seconds (2733.39 seconds total)