Starting phenix.real_space_refine on Thu Jul 2 08:14:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t3r_41009/07_2026/8t3r_41009.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t3r_41009/07_2026/8t3r_41009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t3r_41009/07_2026/8t3r_41009.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t3r_41009/07_2026/8t3r_41009.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t3r_41009/07_2026/8t3r_41009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t3r_41009/07_2026/8t3r_41009.map" } resolution = 2.99 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= -0.001 sd= 0.076 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: 6 Type Number sf(0) Gaussians P 7 5.49 5 S 34 5.16 5 Cl 1 4.86 5 C 5194 2.51 5 N 1207 2.21 5 O 1312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7755 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3527 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 25, 'TRANS': 424} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4037 Classifications: {'peptide': 511} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 481} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 87 Unusual residues: {'NAG': 1, 'PIO': 1, 'PLC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 103 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'NAG': 1, 'PIO': 1, 'PLC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.81, per 1000 atoms: 0.23 Number of scatterers: 7755 At special positions: 0 Unit cell: (85.32, 75.6, 128.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 34 16.00 P 7 15.00 O 1312 8.00 N 1207 7.00 C 5194 6.00 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 Links applied NAG-ASN " NAG A1001 " - " ASN A 642 " " NAG B1001 " - " ASN B 642 " Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 390.5 milliseconds 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1790 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 3 sheets defined 75.5% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 404 through 431 removed outlier: 3.978A pdb=" N ILE A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) Proline residue: A 419 - end of helix removed outlier: 3.684A pdb=" N GLY A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 455 Processing helix chain 'A' and resid 465 through 483 Processing helix chain 'A' and resid 485 through 507 removed outlier: 3.708A pdb=" N GLY A 489 " --> pdb=" O GLU A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 547 removed outlier: 3.691A pdb=" N ILE A 533 " --> pdb=" O SER A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 593 removed outlier: 3.853A pdb=" N ASN A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 608 Processing helix chain 'A' and resid 608 through 623 Processing helix chain 'A' and resid 660 through 666 removed outlier: 3.657A pdb=" N MET A 664 " --> pdb=" O PRO A 660 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE A 665 " --> pdb=" O ILE A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 685 removed outlier: 3.858A pdb=" N LEU A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU A 681 " --> pdb=" O LEU A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 718 removed outlier: 3.920A pdb=" N LEU A 718 " --> pdb=" O GLY A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 773 Processing helix chain 'A' and resid 776 through 782 Processing helix chain 'A' and resid 784 through 801 removed outlier: 3.866A pdb=" N LEU A 788 " --> pdb=" O PRO A 784 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A 801 " --> pdb=" O VAL A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 814 removed outlier: 4.125A pdb=" N PHE A 813 " --> pdb=" O ILE A 809 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 819 removed outlier: 3.595A pdb=" N HIS A 819 " --> pdb=" O PRO A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 827 Processing helix chain 'A' and resid 829 through 853 Processing helix chain 'A' and resid 855 through 857 No H-bonds generated for 'chain 'A' and resid 855 through 857' Processing helix chain 'A' and resid 858 through 865 Processing helix chain 'A' and resid 865 through 872 Processing helix chain 'A' and resid 873 through 878 removed outlier: 3.584A pdb=" N ILE A 877 " --> pdb=" O LEU A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 887 removed outlier: 3.703A pdb=" N LEU A 883 " --> pdb=" O ARG A 879 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP A 887 " --> pdb=" O LEU A 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 390 Processing helix chain 'B' and resid 392 through 399 Processing helix chain 'B' and resid 402 through 431 removed outlier: 3.646A pdb=" N LEU B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE B 414 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Proline residue: B 419 - end of helix Processing helix chain 'B' and resid 436 through 455 Processing helix chain 'B' and resid 465 through 483 Processing helix chain 'B' and resid 485 through 507 Processing helix chain 'B' and resid 508 through 516 removed outlier: 3.536A pdb=" N ILE B 516 " --> pdb=" O VAL B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 547 Processing helix chain 'B' and resid 570 through 593 removed outlier: 3.797A pdb=" N ASN B 593 " --> pdb=" O ARG B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 608 Processing helix chain 'B' and resid 608 through 623 Processing helix chain 'B' and resid 660 through 667 removed outlier: 3.610A pdb=" N MET B 664 " --> pdb=" O PRO B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 690 Processing helix chain 'B' and resid 691 through 695 Processing helix chain 'B' and resid 702 through 719 removed outlier: 3.661A pdb=" N LEU B 718 " --> pdb=" O GLY B 714 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE B 719 " --> pdb=" O VAL B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 738 Processing helix chain 'B' and resid 761 through 772 Processing helix chain 'B' and resid 773 through 775 No H-bonds generated for 'chain 'B' and resid 773 through 775' Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 784 through 801 removed outlier: 3.840A pdb=" N LEU B 788 " --> pdb=" O PRO B 784 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER B 801 " --> pdb=" O VAL B 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 812 Processing helix chain 'B' and resid 815 through 819 removed outlier: 3.666A pdb=" N HIS B 819 " --> pdb=" O PRO B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 827 Processing helix chain 'B' and resid 829 through 853 Processing helix chain 'B' and resid 855 through 857 No H-bonds generated for 'chain 'B' and resid 855 through 857' Processing helix chain 'B' and resid 858 through 865 Processing helix chain 'B' and resid 865 through 872 removed outlier: 3.535A pdb=" N LEU B 869 " --> pdb=" O LEU B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 878 removed outlier: 3.807A pdb=" N ILE B 877 " --> pdb=" O LEU B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 887 Processing sheet with id=AA1, first strand: chain 'A' and resid 461 through 463 removed outlier: 3.660A pdb=" N GLY A 463 " --> pdb=" O SER A 725 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 462 through 463 Processing sheet with id=AA3, first strand: chain 'B' and resid 739 through 740 removed outlier: 3.975A pdb=" N GLU B 755 " --> pdb=" O VAL B 740 " (cutoff:3.500A) 494 hydrogen bonds defined for protein. 1446 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: 0.98 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1130 1.31 - 1.43: 2124 1.43 - 1.56: 4619 1.56 - 1.68: 10 1.68 - 1.81: 62 Bond restraints: 7945 Sorted by residual: bond pdb=" C1A PIO A1002 " pdb=" O2C PIO A1002 " ideal model delta sigma weight residual 1.332 1.405 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C1A PIO B1002 " pdb=" O2C PIO B1002 " ideal model delta sigma weight residual 1.332 1.404 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C1B PIO A1002 " pdb=" O3C PIO A1002 " ideal model delta sigma weight residual 1.331 1.397 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C1B PIO B1002 " pdb=" O3C PIO B1002 " ideal model delta sigma weight residual 1.331 1.397 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" O4 PIO B1002 " pdb=" P4 PIO B1002 " ideal model delta sigma weight residual 1.710 1.645 0.065 2.00e-02 2.50e+03 1.07e+01 ... (remaining 7940 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 10536 2.49 - 4.99: 195 4.99 - 7.48: 53 7.48 - 9.98: 6 9.98 - 12.47: 5 Bond angle restraints: 10795 Sorted by residual: angle pdb=" O1 PIO A1002 " pdb=" P1 PIO A1002 " pdb=" O13 PIO A1002 " ideal model delta sigma weight residual 97.64 110.11 -12.47 3.00e+00 1.11e-01 1.73e+01 angle pdb=" O1 PIO B1002 " pdb=" P1 PIO B1002 " pdb=" O13 PIO B1002 " ideal model delta sigma weight residual 97.64 109.50 -11.86 3.00e+00 1.11e-01 1.56e+01 angle pdb=" O11 PIO B1002 " pdb=" P1 PIO B1002 " pdb=" O12 PIO B1002 " ideal model delta sigma weight residual 121.09 109.50 11.59 3.00e+00 1.11e-01 1.49e+01 angle pdb=" O11 PIO A1002 " pdb=" P1 PIO A1002 " pdb=" O12 PIO A1002 " ideal model delta sigma weight residual 121.09 109.82 11.27 3.00e+00 1.11e-01 1.41e+01 angle pdb=" N ILE A 498 " pdb=" CA ILE A 498 " pdb=" CB ILE A 498 " ideal model delta sigma weight residual 110.55 114.83 -4.28 1.17e+00 7.31e-01 1.34e+01 ... (remaining 10790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.29: 4403 22.29 - 44.58: 254 44.58 - 66.86: 28 66.86 - 89.15: 8 89.15 - 111.44: 4 Dihedral angle restraints: 4697 sinusoidal: 1926 harmonic: 2771 Sorted by residual: dihedral pdb=" CA VAL B 513 " pdb=" C VAL B 513 " pdb=" N ARG B 514 " pdb=" CA ARG B 514 " ideal model delta harmonic sigma weight residual 180.00 160.46 19.54 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" C3 PLC B1003 " pdb=" C1 PLC B1003 " pdb=" C2 PLC B1003 " pdb=" O3P PLC B1003 " ideal model delta sinusoidal sigma weight residual 67.16 -44.28 111.44 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" O2 PLC B1003 " pdb=" C1 PLC B1003 " pdb=" C2 PLC B1003 " pdb=" O3P PLC B1003 " ideal model delta sinusoidal sigma weight residual -55.71 -166.91 111.20 1 3.00e+01 1.11e-03 1.45e+01 ... (remaining 4694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1171 0.086 - 0.172: 109 0.172 - 0.258: 7 0.258 - 0.344: 1 0.344 - 0.430: 1 Chirality restraints: 1289 Sorted by residual: chirality pdb=" C1 NAG A1001 " pdb=" ND2 ASN A 642 " pdb=" C2 NAG A1001 " pdb=" O5 NAG A1001 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.62e+00 chirality pdb=" CA LEU B 680 " pdb=" N LEU B 680 " pdb=" C LEU B 680 " pdb=" CB LEU B 680 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA SER B 682 " pdb=" N SER B 682 " pdb=" C SER B 682 " pdb=" CB SER B 682 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1286 not shown) Planarity restraints: 1297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 642 " 0.028 2.00e-02 2.50e+03 2.82e-02 9.94e+00 pdb=" CG ASN A 642 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN A 642 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 642 " -0.038 2.00e-02 2.50e+03 pdb=" C1 NAG A1001 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 390 " 0.047 5.00e-02 4.00e+02 7.21e-02 8.33e+00 pdb=" N PRO B 391 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 391 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 391 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 466 " -0.038 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO B 467 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 467 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 467 " -0.032 5.00e-02 4.00e+02 ... (remaining 1294 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1016 2.76 - 3.29: 7366 3.29 - 3.83: 12671 3.83 - 4.36: 14864 4.36 - 4.90: 26042 Nonbonded interactions: 61959 Sorted by model distance: nonbonded pdb=" OE1 GLU A 472 " pdb=" OH TYR A 486 " model vdw 2.220 3.040 nonbonded pdb=" OE1 GLU B 472 " pdb=" OH TYR B 486 " model vdw 2.240 3.040 nonbonded pdb=" O SER A 418 " pdb=" OG1 THR A 422 " model vdw 2.290 3.040 nonbonded pdb=" O PRO A 568 " pdb=" ND2 ASN B 569 " model vdw 2.344 3.120 nonbonded pdb=" NH2 ARG A 490 " pdb=" O MET A 721 " model vdw 2.365 3.120 ... (remaining 61954 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 404 through 888 or (resid 889 and (name N or name CA or na \ me C or name O or name CB )))) selection = (chain 'B' and (resid 404 through 507 or (resid 508 and (name N or name CA or na \ me C or name O or name CB )) or resid 509 through 510 or (resid 511 through 512 \ and (name N or name CA or name C or name O or name CB )) or resid 513 through 58 \ 0 or (resid 581 and (name N or name CA or name C or name O or name CB or name CG \ 2)) or resid 582 through 685 or resid 703 through 729 or (resid 730 and (name N \ or name CA or name C or name O or name CB )) or resid 731 or (resid 732 and (nam \ e N or name CA or name C or name O or name CB )) or resid 733 or (resid 734 thro \ ugh 736 and (name N or name CA or name C or name O or name CB )) or resid 757 th \ rough 889)) } 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: 1.940 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.760 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:6.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 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 0.073 7947 Z= 0.248 Angle : 0.924 12.848 10801 Z= 0.452 Chirality : 0.052 0.430 1289 Planarity : 0.007 0.072 1295 Dihedral : 14.327 111.438 2907 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 951 helix: 0.07 (0.19), residues: 660 sheet: -2.93 (1.25), residues: 10 loop : -1.16 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 782 TYR 0.037 0.002 TYR A 413 PHE 0.032 0.002 PHE A 792 TRP 0.026 0.002 TRP A 492 HIS 0.002 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.25 ( 7945) covalent geometry : angle 0.90912 / 0.45 (10795) hydrogen bonds : bond 0.15873 / 10.66 ( 494) hydrogen bonds : angle 5.80239 / 4.21 ( 1446) link_NAG-ASN : bond 0.00868 / 0.46 ( 2) link_NAG-ASN : angle 7.18170 / 4.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.289 Fit side-chains REVERT: A 413 TYR cc_start: 0.7280 (t80) cc_final: 0.6894 (t80) REVERT: A 587 MET cc_start: 0.8264 (mmt) cc_final: 0.7607 (mmt) REVERT: A 679 PHE cc_start: 0.7499 (t80) cc_final: 0.7156 (t80) REVERT: A 712 MET cc_start: 0.7954 (mtm) cc_final: 0.7693 (mtp) REVERT: B 542 LYS cc_start: 0.8190 (tmmt) cc_final: 0.7964 (ttpt) REVERT: B 821 ASP cc_start: 0.8728 (t0) cc_final: 0.8455 (t0) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.4450 time to fit residues: 57.2213 Evaluate side-chains 99 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 569 ASN B 754 GLN B 884 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.149334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.117679 restraints weight = 9484.299| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.86 r_work: 0.3224 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7947 Z= 0.138 Angle : 0.576 7.348 10801 Z= 0.284 Chirality : 0.043 0.385 1289 Planarity : 0.005 0.057 1295 Dihedral : 8.689 88.878 1158 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.08 % Allowed : 7.59 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.75 (0.27), residues: 951 helix: 1.14 (0.20), residues: 664 sheet: -2.67 (1.40), residues: 10 loop : -0.85 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 432 TYR 0.013 0.001 TYR B 486 PHE 0.021 0.001 PHE A 792 TRP 0.020 0.002 TRP A 492 HIS 0.002 0.000 HIS B 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 7945) covalent geometry : angle 0.56984 / 0.28 (10795) hydrogen bonds : bond 0.05043 / 3.53 ( 494) hydrogen bonds : angle 4.32306 / 3.11 ( 1446) link_NAG-ASN : bond 0.00872 / 0.46 ( 2) link_NAG-ASN : angle 3.62379 / 1.99 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.217 Fit side-chains REVERT: A 451 PHE cc_start: 0.6367 (t80) cc_final: 0.6159 (t80) REVERT: A 679 PHE cc_start: 0.7418 (t80) cc_final: 0.7153 (t80) REVERT: A 681 GLU cc_start: 0.7884 (pt0) cc_final: 0.7467 (pt0) REVERT: A 712 MET cc_start: 0.7913 (mtm) cc_final: 0.7651 (mtp) REVERT: A 776 MET cc_start: 0.6982 (mtt) cc_final: 0.6504 (mtp) REVERT: A 826 LYS cc_start: 0.7532 (mmtt) cc_final: 0.7231 (mmtt) REVERT: B 377 GLN cc_start: 0.6093 (tm-30) cc_final: 0.5827 (tm-30) REVERT: B 499 LEU cc_start: 0.8566 (tp) cc_final: 0.8363 (tm) REVERT: B 512 LEU cc_start: 0.7949 (mt) cc_final: 0.7701 (mt) REVERT: B 542 LYS cc_start: 0.8264 (tmmt) cc_final: 0.7998 (ttpt) outliers start: 9 outliers final: 3 residues processed: 122 average time/residue: 0.4389 time to fit residues: 57.5784 Evaluate side-chains 102 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 853 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 54 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 85 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 521 GLN B 754 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.147553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.115805 restraints weight = 9475.357| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.85 r_work: 0.3181 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7947 Z= 0.160 Angle : 0.576 7.477 10801 Z= 0.283 Chirality : 0.043 0.373 1289 Planarity : 0.005 0.053 1295 Dihedral : 8.415 86.106 1158 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.45 % Allowed : 10.96 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.11 (0.27), residues: 951 helix: 1.41 (0.20), residues: 661 sheet: -2.79 (1.35), residues: 10 loop : -0.67 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 432 TYR 0.016 0.002 TYR B 824 PHE 0.022 0.001 PHE A 792 TRP 0.026 0.002 TRP A 492 HIS 0.002 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 ( 7945) covalent geometry : angle 0.57105 / 0.28 (10795) hydrogen bonds : bond 0.04994 / 3.52 ( 494) hydrogen bonds : angle 4.19500 / 3.01 ( 1446) link_NAG-ASN : bond 0.00719 / 0.38 ( 2) link_NAG-ASN : angle 3.20461 / 1.76 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.220 Fit side-chains REVERT: A 413 TYR cc_start: 0.8279 (t80) cc_final: 0.7830 (t80) REVERT: A 542 LYS cc_start: 0.8309 (tptt) cc_final: 0.7525 (ttmt) REVERT: A 590 LYS cc_start: 0.6888 (OUTLIER) cc_final: 0.5698 (tttm) REVERT: A 679 PHE cc_start: 0.7489 (t80) cc_final: 0.7140 (t80) REVERT: A 681 GLU cc_start: 0.7744 (pt0) cc_final: 0.7373 (pt0) REVERT: A 776 MET cc_start: 0.6993 (mtt) cc_final: 0.6466 (mtp) REVERT: A 868 PRO cc_start: 0.7911 (Cg_exo) cc_final: 0.7650 (Cg_endo) REVERT: B 377 GLN cc_start: 0.6047 (tm-30) cc_final: 0.5814 (tm-30) REVERT: B 512 LEU cc_start: 0.7940 (mt) cc_final: 0.7699 (mt) outliers start: 12 outliers final: 7 residues processed: 120 average time/residue: 0.4826 time to fit residues: 61.9835 Evaluate side-chains 110 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 779 ILE Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 864 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 73 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 754 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.148488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.116807 restraints weight = 9555.384| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.86 r_work: 0.3141 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7947 Z= 0.122 Angle : 0.537 7.746 10801 Z= 0.264 Chirality : 0.041 0.328 1289 Planarity : 0.005 0.052 1295 Dihedral : 8.153 80.030 1158 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.33 % Allowed : 14.22 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.39 (0.27), residues: 951 helix: 1.63 (0.20), residues: 665 sheet: None (None), residues: 0 loop : -0.72 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 432 TYR 0.013 0.001 TYR A 824 PHE 0.016 0.001 PHE A 792 TRP 0.021 0.001 TRP A 492 HIS 0.001 0.000 HIS B 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 7945) covalent geometry : angle 0.53378 / 0.26 (10795) hydrogen bonds : bond 0.04421 / 3.13 ( 494) hydrogen bonds : angle 4.02152 / 2.88 ( 1446) link_NAG-ASN : bond 0.00691 / 0.36 ( 2) link_NAG-ASN : angle 2.61254 / 1.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.271 Fit side-chains REVERT: A 413 TYR cc_start: 0.8270 (t80) cc_final: 0.7536 (t80) REVERT: A 473 GLU cc_start: 0.7808 (tp30) cc_final: 0.7413 (tm-30) REVERT: A 542 LYS cc_start: 0.8247 (tptt) cc_final: 0.7573 (ttmm) REVERT: A 590 LYS cc_start: 0.6817 (OUTLIER) cc_final: 0.5651 (tttt) REVERT: A 679 PHE cc_start: 0.7391 (t80) cc_final: 0.7011 (t80) REVERT: A 681 GLU cc_start: 0.7589 (pt0) cc_final: 0.7324 (pt0) REVERT: A 776 MET cc_start: 0.6770 (mtt) cc_final: 0.6481 (mtp) REVERT: A 777 GLU cc_start: 0.6660 (tp30) cc_final: 0.6443 (tp30) REVERT: A 826 LYS cc_start: 0.7582 (mmtt) cc_final: 0.7156 (mmtt) REVERT: A 868 PRO cc_start: 0.7647 (Cg_exo) cc_final: 0.7405 (Cg_endo) REVERT: B 377 GLN cc_start: 0.6000 (tm-30) cc_final: 0.5740 (tm-30) REVERT: B 499 LEU cc_start: 0.8465 (tp) cc_final: 0.8246 (tm) REVERT: B 512 LEU cc_start: 0.7839 (mt) cc_final: 0.7603 (mt) REVERT: B 672 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7234 (mp) outliers start: 11 outliers final: 5 residues processed: 118 average time/residue: 0.4752 time to fit residues: 60.1115 Evaluate side-chains 122 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 853 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 58 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 1 optimal weight: 0.2980 chunk 87 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 94 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 64 optimal weight: 0.0270 chunk 81 optimal weight: 1.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 754 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.150866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.119432 restraints weight = 9414.851| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.85 r_work: 0.3197 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7947 Z= 0.104 Angle : 0.509 8.021 10801 Z= 0.250 Chirality : 0.040 0.296 1289 Planarity : 0.004 0.051 1295 Dihedral : 7.767 70.251 1158 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.33 % Allowed : 15.30 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.71 (0.28), residues: 951 helix: 1.89 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.66 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 432 TYR 0.011 0.001 TYR B 534 PHE 0.013 0.001 PHE B 471 TRP 0.016 0.001 TRP A 492 HIS 0.001 0.000 HIS B 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 7945) covalent geometry : angle 0.50663 / 0.25 (10795) hydrogen bonds : bond 0.03933 / 2.78 ( 494) hydrogen bonds : angle 3.85975 / 2.76 ( 1446) link_NAG-ASN : bond 0.00684 / 0.36 ( 2) link_NAG-ASN : angle 2.22590 / 1.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.198 Fit side-chains REVERT: A 413 TYR cc_start: 0.8315 (t80) cc_final: 0.7531 (t80) REVERT: A 497 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6373 (mt) REVERT: A 542 LYS cc_start: 0.8243 (tptt) cc_final: 0.7573 (ttmm) REVERT: A 590 LYS cc_start: 0.7029 (OUTLIER) cc_final: 0.5850 (tttt) REVERT: A 679 PHE cc_start: 0.7426 (t80) cc_final: 0.7037 (t80) REVERT: A 776 MET cc_start: 0.6746 (mtt) cc_final: 0.6415 (mtp) REVERT: A 826 LYS cc_start: 0.7533 (mmtt) cc_final: 0.7247 (mmtt) REVERT: A 868 PRO cc_start: 0.7641 (Cg_exo) cc_final: 0.7416 (Cg_endo) REVERT: B 377 GLN cc_start: 0.6054 (tm-30) cc_final: 0.5789 (tm-30) REVERT: B 399 ASP cc_start: 0.8058 (t0) cc_final: 0.7270 (t0) REVERT: B 512 LEU cc_start: 0.7845 (mt) cc_final: 0.7615 (mt) REVERT: B 672 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7225 (mp) REVERT: B 821 ASP cc_start: 0.8803 (t0) cc_final: 0.8589 (t0) outliers start: 11 outliers final: 5 residues processed: 126 average time/residue: 0.4795 time to fit residues: 64.6312 Evaluate side-chains 118 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 801 SER Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 853 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 56 optimal weight: 3.9990 chunk 63 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 30 optimal weight: 0.0030 chunk 50 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 754 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.151748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.120414 restraints weight = 9411.617| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.85 r_work: 0.3161 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7947 Z= 0.106 Angle : 0.525 8.269 10801 Z= 0.257 Chirality : 0.040 0.289 1289 Planarity : 0.004 0.050 1295 Dihedral : 7.570 62.882 1158 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.57 % Allowed : 15.90 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.78 (0.28), residues: 951 helix: 1.94 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -0.68 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 432 TYR 0.012 0.001 TYR A 824 PHE 0.020 0.001 PHE A 478 TRP 0.013 0.001 TRP A 492 HIS 0.001 0.000 HIS B 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 7945) covalent geometry : angle 0.52290 / 0.26 (10795) hydrogen bonds : bond 0.03875 / 2.74 ( 494) hydrogen bonds : angle 3.81678 / 2.73 ( 1446) link_NAG-ASN : bond 0.00661 / 0.35 ( 2) link_NAG-ASN : angle 2.10922 / 1.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.292 Fit side-chains REVERT: A 413 TYR cc_start: 0.8292 (t80) cc_final: 0.7498 (t80) REVERT: A 473 GLU cc_start: 0.7813 (tp30) cc_final: 0.7406 (tm-30) REVERT: A 497 LEU cc_start: 0.6446 (OUTLIER) cc_final: 0.6217 (mt) REVERT: A 590 LYS cc_start: 0.6888 (OUTLIER) cc_final: 0.5674 (tttt) REVERT: A 679 PHE cc_start: 0.7354 (t80) cc_final: 0.6961 (t80) REVERT: A 776 MET cc_start: 0.6619 (mtt) cc_final: 0.6195 (mtp) REVERT: A 826 LYS cc_start: 0.7472 (mmtt) cc_final: 0.7152 (mptp) REVERT: A 868 PRO cc_start: 0.7505 (Cg_exo) cc_final: 0.7290 (Cg_endo) REVERT: B 377 GLN cc_start: 0.5972 (tm-30) cc_final: 0.5691 (tm-30) REVERT: B 399 ASP cc_start: 0.8001 (t0) cc_final: 0.7159 (t0) REVERT: B 499 LEU cc_start: 0.8378 (tp) cc_final: 0.8157 (tm) REVERT: B 512 LEU cc_start: 0.7739 (mt) cc_final: 0.7511 (mt) REVERT: B 551 LYS cc_start: 0.8305 (tptt) cc_final: 0.7854 (mtpp) REVERT: B 587 MET cc_start: 0.7628 (mmp) cc_final: 0.7416 (mmp) REVERT: B 672 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7249 (mt) REVERT: B 821 ASP cc_start: 0.8769 (t0) cc_final: 0.8554 (t0) outliers start: 13 outliers final: 7 residues processed: 121 average time/residue: 0.4977 time to fit residues: 64.3239 Evaluate side-chains 120 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 801 SER Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 864 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 58 optimal weight: 0.0980 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 54 optimal weight: 0.0870 chunk 39 optimal weight: 0.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 754 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.151066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.119496 restraints weight = 9379.608| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.85 r_work: 0.3149 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7947 Z= 0.113 Angle : 0.529 8.393 10801 Z= 0.259 Chirality : 0.041 0.291 1289 Planarity : 0.004 0.050 1295 Dihedral : 7.462 56.085 1158 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.81 % Allowed : 16.14 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.82 (0.28), residues: 951 helix: 2.00 (0.20), residues: 661 sheet: None (None), residues: 0 loop : -0.67 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 432 TYR 0.012 0.001 TYR A 824 PHE 0.013 0.001 PHE A 478 TRP 0.015 0.001 TRP A 492 HIS 0.001 0.000 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 7945) covalent geometry : angle 0.52632 / 0.26 (10795) hydrogen bonds : bond 0.03977 / 2.82 ( 494) hydrogen bonds : angle 3.82519 / 2.73 ( 1446) link_NAG-ASN : bond 0.00628 / 0.33 ( 2) link_NAG-ASN : angle 2.11589 / 1.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.299 Fit side-chains REVERT: A 413 TYR cc_start: 0.8363 (t80) cc_final: 0.7589 (t80) REVERT: A 473 GLU cc_start: 0.7826 (tp30) cc_final: 0.7464 (tm-30) REVERT: A 497 LEU cc_start: 0.6421 (OUTLIER) cc_final: 0.6191 (mt) REVERT: A 542 LYS cc_start: 0.8180 (tptt) cc_final: 0.7311 (ttmt) REVERT: A 590 LYS cc_start: 0.6916 (OUTLIER) cc_final: 0.5625 (tttt) REVERT: A 608 PHE cc_start: 0.7336 (m-80) cc_final: 0.7136 (m-10) REVERT: A 664 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.7228 (mpp) REVERT: A 679 PHE cc_start: 0.7336 (t80) cc_final: 0.6887 (t80) REVERT: A 776 MET cc_start: 0.6529 (mtt) cc_final: 0.6195 (mtp) REVERT: A 868 PRO cc_start: 0.7511 (Cg_exo) cc_final: 0.7296 (Cg_endo) REVERT: B 377 GLN cc_start: 0.5975 (tm-30) cc_final: 0.5658 (tm-30) REVERT: B 399 ASP cc_start: 0.7968 (t0) cc_final: 0.7099 (t0) REVERT: B 499 LEU cc_start: 0.8414 (tp) cc_final: 0.8191 (tm) REVERT: B 512 LEU cc_start: 0.7731 (mt) cc_final: 0.7510 (mt) REVERT: B 551 LYS cc_start: 0.8383 (tptt) cc_final: 0.7900 (mtpp) REVERT: B 672 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7279 (mt) REVERT: B 712 MET cc_start: 0.8654 (mtm) cc_final: 0.8186 (mtm) REVERT: B 721 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.7454 (mmt) REVERT: B 741 MET cc_start: 0.8174 (mmt) cc_final: 0.7878 (tpt) REVERT: B 821 ASP cc_start: 0.8763 (t0) cc_final: 0.8545 (t0) outliers start: 15 outliers final: 9 residues processed: 123 average time/residue: 0.4839 time to fit residues: 63.9714 Evaluate side-chains 123 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 801 SER Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 864 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 45 optimal weight: 0.8980 chunk 64 optimal weight: 0.0010 chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 754 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.150165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.118833 restraints weight = 9461.917| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.82 r_work: 0.3246 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7947 Z= 0.114 Angle : 0.524 7.617 10801 Z= 0.255 Chirality : 0.041 0.290 1289 Planarity : 0.004 0.050 1295 Dihedral : 7.391 59.641 1158 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.81 % Allowed : 16.51 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.85 (0.28), residues: 951 helix: 2.03 (0.20), residues: 661 sheet: None (None), residues: 0 loop : -0.65 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 432 TYR 0.012 0.001 TYR A 824 PHE 0.013 0.001 PHE A 792 TRP 0.014 0.001 TRP A 492 HIS 0.001 0.000 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 7945) covalent geometry : angle 0.52169 / 0.25 (10795) hydrogen bonds : bond 0.04005 / 2.84 ( 494) hydrogen bonds : angle 3.77492 / 2.70 ( 1446) link_NAG-ASN : bond 0.00610 / 0.32 ( 2) link_NAG-ASN : angle 2.08629 / 1.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.303 Fit side-chains REVERT: A 413 TYR cc_start: 0.8394 (t80) cc_final: 0.7693 (t80) REVERT: A 473 GLU cc_start: 0.7851 (tp30) cc_final: 0.7501 (tt0) REVERT: A 497 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6754 (mt) REVERT: A 542 LYS cc_start: 0.8243 (tptt) cc_final: 0.7414 (ttmt) REVERT: A 590 LYS cc_start: 0.7067 (OUTLIER) cc_final: 0.5687 (tttt) REVERT: A 608 PHE cc_start: 0.7500 (m-80) cc_final: 0.7291 (m-10) REVERT: A 664 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7293 (mpp) REVERT: A 679 PHE cc_start: 0.7431 (t80) cc_final: 0.6967 (t80) REVERT: A 776 MET cc_start: 0.6637 (mtt) cc_final: 0.6266 (mtp) REVERT: A 868 PRO cc_start: 0.7633 (Cg_exo) cc_final: 0.7418 (Cg_endo) REVERT: B 377 GLN cc_start: 0.6041 (tm-30) cc_final: 0.5719 (tm-30) REVERT: B 399 ASP cc_start: 0.8097 (t0) cc_final: 0.7202 (t0) REVERT: B 499 LEU cc_start: 0.8562 (tp) cc_final: 0.8344 (tm) REVERT: B 512 LEU cc_start: 0.7835 (mt) cc_final: 0.7612 (mt) REVERT: B 551 LYS cc_start: 0.8434 (tptt) cc_final: 0.7948 (mtpp) REVERT: B 672 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7344 (mp) REVERT: B 721 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.7669 (mmt) REVERT: B 741 MET cc_start: 0.8172 (mmt) cc_final: 0.7520 (mmm) REVERT: B 821 ASP cc_start: 0.8767 (t0) cc_final: 0.8538 (t0) outliers start: 15 outliers final: 8 residues processed: 119 average time/residue: 0.4808 time to fit residues: 61.4106 Evaluate side-chains 124 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 801 SER Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 864 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 68 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 37 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 0.0570 chunk 22 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.151108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.119548 restraints weight = 9364.319| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.86 r_work: 0.3187 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7947 Z= 0.109 Angle : 0.530 8.343 10801 Z= 0.255 Chirality : 0.041 0.283 1289 Planarity : 0.004 0.050 1295 Dihedral : 7.313 64.090 1158 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.81 % Allowed : 16.51 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.99 (0.28), residues: 951 helix: 2.15 (0.20), residues: 653 sheet: None (None), residues: 0 loop : -0.57 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 432 TYR 0.012 0.001 TYR A 824 PHE 0.012 0.001 PHE A 792 TRP 0.016 0.001 TRP A 492 HIS 0.001 0.000 HIS B 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 7945) covalent geometry : angle 0.52794 / 0.25 (10795) hydrogen bonds : bond 0.03922 / 2.77 ( 494) hydrogen bonds : angle 3.75091 / 2.68 ( 1446) link_NAG-ASN : bond 0.00607 / 0.32 ( 2) link_NAG-ASN : angle 2.00780 / 1.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.315 Fit side-chains REVERT: A 413 TYR cc_start: 0.8376 (t80) cc_final: 0.7663 (t80) REVERT: A 473 GLU cc_start: 0.7845 (tp30) cc_final: 0.7474 (tm-30) REVERT: A 497 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6662 (mt) REVERT: A 542 LYS cc_start: 0.8216 (tptt) cc_final: 0.7369 (ttmt) REVERT: A 590 LYS cc_start: 0.7055 (OUTLIER) cc_final: 0.5655 (tttt) REVERT: A 608 PHE cc_start: 0.7395 (m-80) cc_final: 0.7186 (m-10) REVERT: A 664 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.7073 (mpp) REVERT: A 679 PHE cc_start: 0.7493 (t80) cc_final: 0.7039 (t80) REVERT: A 776 MET cc_start: 0.6552 (mtt) cc_final: 0.6183 (mtp) REVERT: A 868 PRO cc_start: 0.7488 (Cg_exo) cc_final: 0.7254 (Cg_endo) REVERT: B 377 GLN cc_start: 0.6016 (tm-30) cc_final: 0.5685 (tm-30) REVERT: B 399 ASP cc_start: 0.8007 (t0) cc_final: 0.7106 (t0) REVERT: B 499 LEU cc_start: 0.8466 (tp) cc_final: 0.8243 (tm) REVERT: B 512 LEU cc_start: 0.7769 (mt) cc_final: 0.7550 (mt) REVERT: B 551 LYS cc_start: 0.8413 (tptt) cc_final: 0.7990 (mtpp) REVERT: B 672 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7226 (mp) REVERT: B 741 MET cc_start: 0.8034 (mmt) cc_final: 0.7723 (tpp) REVERT: B 821 ASP cc_start: 0.8779 (t0) cc_final: 0.8573 (t0) outliers start: 15 outliers final: 9 residues processed: 116 average time/residue: 0.4949 time to fit residues: 61.5356 Evaluate side-chains 119 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 801 SER Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 779 ILE Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 864 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.9980 chunk 53 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 84 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 754 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.150371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.118837 restraints weight = 9413.671| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.86 r_work: 0.3199 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7947 Z= 0.120 Angle : 0.546 7.752 10801 Z= 0.263 Chirality : 0.041 0.290 1289 Planarity : 0.004 0.049 1295 Dihedral : 7.257 66.119 1158 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.69 % Allowed : 16.99 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.85 (0.28), residues: 951 helix: 2.02 (0.20), residues: 661 sheet: None (None), residues: 0 loop : -0.64 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 432 TYR 0.012 0.001 TYR A 824 PHE 0.028 0.001 PHE A 411 TRP 0.017 0.001 TRP A 492 HIS 0.001 0.000 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 7945) covalent geometry : angle 0.54388 / 0.26 (10795) hydrogen bonds : bond 0.04053 / 2.86 ( 494) hydrogen bonds : angle 3.79523 / 2.71 ( 1446) link_NAG-ASN : bond 0.00589 / 0.31 ( 2) link_NAG-ASN : angle 2.07317 / 1.15 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.292 Fit side-chains REVERT: A 413 TYR cc_start: 0.8375 (t80) cc_final: 0.7675 (t80) REVERT: A 473 GLU cc_start: 0.7826 (tp30) cc_final: 0.7455 (tm-30) REVERT: A 484 LEU cc_start: 0.7317 (mp) cc_final: 0.7002 (pp) REVERT: A 497 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6704 (mt) REVERT: A 542 LYS cc_start: 0.8236 (tptt) cc_final: 0.7396 (ttmt) REVERT: A 590 LYS cc_start: 0.7043 (OUTLIER) cc_final: 0.5653 (tttt) REVERT: A 664 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.7098 (mpp) REVERT: A 776 MET cc_start: 0.6581 (mtt) cc_final: 0.6195 (mtp) REVERT: A 868 PRO cc_start: 0.7539 (Cg_exo) cc_final: 0.7300 (Cg_endo) REVERT: B 399 ASP cc_start: 0.8033 (t0) cc_final: 0.7139 (t0) REVERT: B 499 LEU cc_start: 0.8507 (tp) cc_final: 0.8279 (tm) REVERT: B 512 LEU cc_start: 0.7807 (mt) cc_final: 0.7585 (mt) REVERT: B 672 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7288 (mp) REVERT: B 721 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.7450 (mmt) REVERT: B 741 MET cc_start: 0.8087 (mmt) cc_final: 0.7761 (tpp) REVERT: B 821 ASP cc_start: 0.8772 (t0) cc_final: 0.8552 (t0) outliers start: 14 outliers final: 9 residues processed: 115 average time/residue: 0.4834 time to fit residues: 59.7136 Evaluate side-chains 124 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 801 SER Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 779 ILE Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 864 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 90 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 447 GLN B 754 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.146201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.114245 restraints weight = 9374.867| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.85 r_work: 0.3114 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7947 Z= 0.185 Angle : 0.611 7.648 10801 Z= 0.296 Chirality : 0.044 0.346 1289 Planarity : 0.005 0.049 1295 Dihedral : 7.684 63.780 1158 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.81 % Allowed : 16.75 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.51 (0.27), residues: 951 helix: 1.71 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.66 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 384 TYR 0.020 0.002 TYR B 824 PHE 0.017 0.002 PHE A 792 TRP 0.019 0.002 TRP A 492 HIS 0.002 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.18 ( 7945) covalent geometry : angle 0.60823 / 0.30 (10795) hydrogen bonds : bond 0.04974 / 3.51 ( 494) hydrogen bonds : angle 4.04316 / 2.90 ( 1446) link_NAG-ASN : bond 0.00533 / 0.28 ( 2) link_NAG-ASN : angle 2.63009 / 1.45 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2512.66 seconds wall clock time: 43 minutes 43.94 seconds (2623.94 seconds total)