Starting phenix.real_space_refine on Fri Aug 22 18:22:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sxt_40858/08_2025/8sxt_40858.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sxt_40858/08_2025/8sxt_40858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sxt_40858/08_2025/8sxt_40858.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sxt_40858/08_2025/8sxt_40858.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sxt_40858/08_2025/8sxt_40858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sxt_40858/08_2025/8sxt_40858.map" } resolution = 3.3 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= 0.002 sd= 0.032 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 20 5.49 5 Mg 1 5.21 5 S 20 5.16 5 C 4061 2.51 5 N 1080 2.21 5 O 1200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6382 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 225 Classifications: {'RNA': 11} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' U%5*END:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 5987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5987 Classifications: {'peptide': 726} Link IDs: {'PTRANS': 33, 'TRANS': 692} Chain breaks: 1 Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'TTP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.83, per 1000 atoms: 0.29 Number of scatterers: 6382 At special positions: 0 Unit cell: (92.02, 87.72, 110.94, 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) S 20 16.00 P 20 15.00 Mg 1 11.99 O 1200 8.00 N 1080 7.00 C 4061 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 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 344.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 4 sheets defined 64.0% alpha, 5.1% beta 5 base pairs and 7 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 255 through 258 Processing helix chain 'A' and resid 259 through 275 Processing helix chain 'A' and resid 283 through 310 Processing helix chain 'A' and resid 403 through 419 removed outlier: 3.644A pdb=" N GLN A 408 " --> pdb=" O PRO A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 435 removed outlier: 3.685A pdb=" N ASP A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 450 Processing helix chain 'A' and resid 455 through 463 removed outlier: 3.749A pdb=" N VAL A 459 " --> pdb=" O GLY A 455 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 484 removed outlier: 3.687A pdb=" N TYR A 481 " --> pdb=" O THR A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 503 removed outlier: 3.625A pdb=" N LEU A 488 " --> pdb=" O TYR A 484 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix removed outlier: 4.233A pdb=" N LYS A 494 " --> pdb=" O PRO A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 511 removed outlier: 3.768A pdb=" N TYR A 510 " --> pdb=" O ASN A 507 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 511 " --> pdb=" O SER A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 537 through 559 removed outlier: 4.445A pdb=" N HIS A 554 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LYS A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 589 removed outlier: 3.889A pdb=" N ILE A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 608 removed outlier: 3.990A pdb=" N ILE A 608 " --> pdb=" O PHE A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 620 Processing helix chain 'A' and resid 624 through 634 removed outlier: 3.619A pdb=" N ALA A 632 " --> pdb=" O LYS A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 682 removed outlier: 3.624A pdb=" N VAL A 674 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 730 removed outlier: 4.483A pdb=" N GLN A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.741A pdb=" N GLU A 750 " --> pdb=" O ASN A 746 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER A 751 " --> pdb=" O ARG A 747 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN A 752 " --> pdb=" O GLN A 748 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 753 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 778 No H-bonds generated for 'chain 'A' and resid 776 through 778' Processing helix chain 'A' and resid 779 through 785 Processing helix chain 'A' and resid 785 through 799 removed outlier: 3.711A pdb=" N ASN A 797 " --> pdb=" O LYS A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 817 Processing helix chain 'A' and resid 817 through 828 Processing helix chain 'A' and resid 833 through 850 removed outlier: 4.042A pdb=" N PHE A 837 " --> pdb=" O PRO A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 863 Processing helix chain 'A' and resid 864 through 868 Processing helix chain 'A' and resid 874 through 885 Processing helix chain 'A' and resid 885 through 893 removed outlier: 4.249A pdb=" N TYR A 889 " --> pdb=" O LYS A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 902 Processing helix chain 'A' and resid 911 through 915 removed outlier: 3.646A pdb=" N LEU A 915 " --> pdb=" O TYR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 947 Processing helix chain 'A' and resid 961 through 966 removed outlier: 3.870A pdb=" N LYS A 965 " --> pdb=" O SER A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 981 removed outlier: 4.126A pdb=" N ILE A 974 " --> pdb=" O LYS A 970 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS A 975 " --> pdb=" O PRO A 971 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A 976 " --> pdb=" O LYS A 972 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 977 " --> pdb=" O THR A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 989 removed outlier: 4.033A pdb=" N ILE A 988 " --> pdb=" O THR A 984 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY A 989 " --> pdb=" O ILE A 985 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 984 through 989' Processing helix chain 'A' and resid 990 through 994 removed outlier: 3.923A pdb=" N PHE A 994 " --> pdb=" O GLY A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1005 Processing helix chain 'A' and resid 1006 through 1008 No H-bonds generated for 'chain 'A' and resid 1006 through 1008' Processing helix chain 'A' and resid 1009 through 1022 removed outlier: 3.733A pdb=" N LYS A1015 " --> pdb=" O TRP A1011 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA A1022 " --> pdb=" O SER A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1030 Processing helix chain 'A' and resid 1034 through 1041 removed outlier: 3.575A pdb=" N PHE A1040 " --> pdb=" O TRP A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1061 Processing sheet with id=AA1, first strand: chain 'A' and resid 530 through 535 removed outlier: 6.050A pdb=" N ILE A 514 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 697 through 698 removed outlier: 3.506A pdb=" N MET A 704 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN A 739 " --> pdb=" O SER A 598 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 740 " --> pdb=" O THR A 760 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 689 through 690 Processing sheet with id=AA4, first strand: chain 'A' and resid 767 through 768 285 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 7 stacking parallelities Total time for adding SS restraints: 1.08 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1001 1.32 - 1.44: 1772 1.44 - 1.57: 3710 1.57 - 1.69: 38 1.69 - 1.82: 34 Bond restraints: 6555 Sorted by residual: bond pdb=" C PRO A 518 " pdb=" O PRO A 518 " ideal model delta sigma weight residual 1.233 1.197 0.036 1.23e-02 6.61e+03 8.78e+00 bond pdb=" C ILE A 517 " pdb=" N PRO A 518 " ideal model delta sigma weight residual 1.331 1.357 -0.026 1.20e-02 6.94e+03 4.71e+00 bond pdb=" CA LYS A 519 " pdb=" C LYS A 519 " ideal model delta sigma weight residual 1.523 1.504 0.018 1.28e-02 6.10e+03 2.08e+00 bond pdb=" CA LYS A 519 " pdb=" CB LYS A 519 " ideal model delta sigma weight residual 1.526 1.511 0.016 1.36e-02 5.41e+03 1.30e+00 bond pdb=" N PRO A 518 " pdb=" CA PRO A 518 " ideal model delta sigma weight residual 1.468 1.455 0.013 1.20e-02 6.94e+03 1.15e+00 ... (remaining 6550 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 8889 3.14 - 6.27: 39 6.27 - 9.41: 1 9.41 - 12.55: 2 12.55 - 15.68: 1 Bond angle restraints: 8932 Sorted by residual: angle pdb=" C ILE A 517 " pdb=" N PRO A 518 " pdb=" CA PRO A 518 " ideal model delta sigma weight residual 119.83 135.51 -15.68 1.08e+00 8.57e-01 2.11e+02 angle pdb=" CB MET A 625 " pdb=" CG MET A 625 " pdb=" SD MET A 625 " ideal model delta sigma weight residual 112.70 125.03 -12.33 3.00e+00 1.11e-01 1.69e+01 angle pdb=" O ILE A 517 " pdb=" C ILE A 517 " pdb=" N PRO A 518 " ideal model delta sigma weight residual 121.10 125.42 -4.32 1.14e+00 7.69e-01 1.43e+01 angle pdb=" N PRO A 518 " pdb=" CA PRO A 518 " pdb=" C PRO A 518 " ideal model delta sigma weight residual 111.03 105.99 5.04 1.54e+00 4.22e-01 1.07e+01 angle pdb=" C LEU A 488 " pdb=" N VAL A 489 " pdb=" CA VAL A 489 " ideal model delta sigma weight residual 120.33 122.72 -2.39 8.00e-01 1.56e+00 8.94e+00 ... (remaining 8927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.59: 3729 29.59 - 59.17: 241 59.17 - 88.76: 19 88.76 - 118.34: 2 118.34 - 147.93: 1 Dihedral angle restraints: 3992 sinusoidal: 1844 harmonic: 2148 Sorted by residual: dihedral pdb=" C2 TTP C 101 " pdb=" C1' TTP C 101 " pdb=" N1 TTP C 101 " pdb=" O4' TTP C 101 " ideal model delta sinusoidal sigma weight residual 301.68 153.76 147.93 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" O5' TTP C 101 " pdb=" O3A TTP C 101 " pdb=" PA TTP C 101 " pdb=" PB TTP C 101 " ideal model delta sinusoidal sigma weight residual 180.02 95.33 84.69 1 2.00e+01 2.50e-03 2.18e+01 dihedral pdb=" CB GLU A 310 " pdb=" CG GLU A 310 " pdb=" CD GLU A 310 " pdb=" OE1 GLU A 310 " ideal model delta sinusoidal sigma weight residual 0.00 -89.01 89.01 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 3989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 584 0.025 - 0.051: 253 0.051 - 0.076: 100 0.076 - 0.102: 45 0.102 - 0.127: 17 Chirality restraints: 999 Sorted by residual: chirality pdb=" CA ILE A 596 " pdb=" N ILE A 596 " pdb=" C ILE A 596 " pdb=" CB ILE A 596 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CA SER A 664 " pdb=" N SER A 664 " pdb=" C SER A 664 " pdb=" CB SER A 664 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA PRO A 490 " pdb=" N PRO A 490 " pdb=" C PRO A 490 " pdb=" CB PRO A 490 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 996 not shown) Planarity restraints: 1050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 908 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO A 909 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 909 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 909 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 813 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C VAL A 813 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL A 813 " -0.010 2.00e-02 2.50e+03 pdb=" N LYS A 814 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 799 " -0.011 2.00e-02 2.50e+03 9.11e-03 2.08e+00 pdb=" CG TRP A 799 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A 799 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 799 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 799 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 799 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 799 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 799 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 799 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 799 " 0.002 2.00e-02 2.50e+03 ... (remaining 1047 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 80 2.61 - 3.18: 5443 3.18 - 3.76: 10039 3.76 - 4.33: 12997 4.33 - 4.90: 21343 Nonbonded interactions: 49902 Sorted by model distance: nonbonded pdb=" O ALA A 601 " pdb="MG MG A1301 " model vdw 2.039 2.170 nonbonded pdb=" O SER A 508 " pdb=" ND2 ASN A 537 " model vdw 2.293 3.120 nonbonded pdb=" O GLN A 748 " pdb=" NE2 GLN A 752 " model vdw 2.299 3.120 nonbonded pdb=" O ALA A 540 " pdb=" ND2 ASN A 544 " model vdw 2.303 3.120 nonbonded pdb=" ND2 ASN A 442 " pdb=" OE2 GLU A 445 " model vdw 2.313 3.120 ... (remaining 49897 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.010 Normalize map: mean=0, sd=1: 0.920 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: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.830 Find NCS groups from input model: 0.040 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 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 : 0.003 0.050 6555 Z= 0.129 Angle : 0.600 15.684 8932 Z= 0.342 Chirality : 0.038 0.127 999 Planarity : 0.003 0.043 1050 Dihedral : 17.793 147.928 2596 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.74 % Favored : 96.12 % Rotamer: Outliers : 0.45 % Allowed : 27.90 % Favored : 71.64 % 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 aren not related in a simple way. whole: 0.31 (0.32), residues: 722 helix: 1.09 (0.28), residues: 376 sheet: -0.83 (0.83), residues: 42 loop : -0.70 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 809 TYR 0.007 0.001 TYR A 484 PHE 0.012 0.001 PHE A 496 TRP 0.025 0.001 TRP A 799 HIS 0.004 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6555) covalent geometry : angle 0.59989 ( 8932) hydrogen bonds : bond 0.17166 ( 298) hydrogen bonds : angle 6.25034 ( 842) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 211 time to evaluate : 0.215 Fit side-chains REVERT: A 286 ASN cc_start: 0.7995 (m110) cc_final: 0.7751 (p0) REVERT: A 422 LYS cc_start: 0.8418 (tttt) cc_final: 0.7824 (ttmt) REVERT: A 457 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7413 (mt-10) REVERT: A 458 ILE cc_start: 0.8548 (mt) cc_final: 0.8271 (tt) REVERT: A 468 LYS cc_start: 0.8648 (mmmm) cc_final: 0.8397 (mmmm) REVERT: A 494 LYS cc_start: 0.8207 (mtmt) cc_final: 0.7771 (ptpt) REVERT: A 502 GLU cc_start: 0.7289 (tp30) cc_final: 0.6727 (tp30) REVERT: A 555 ILE cc_start: 0.8016 (tp) cc_final: 0.7690 (tp) REVERT: A 618 ASN cc_start: 0.8222 (t0) cc_final: 0.7921 (t0) REVERT: A 631 ARG cc_start: 0.7915 (ttm-80) cc_final: 0.7646 (ttp80) REVERT: A 677 ARG cc_start: 0.8115 (mtt90) cc_final: 0.7694 (mtt-85) REVERT: A 681 GLN cc_start: 0.7897 (mm110) cc_final: 0.7615 (mm110) REVERT: A 686 LYS cc_start: 0.8068 (ttmt) cc_final: 0.7811 (ttmm) REVERT: A 704 MET cc_start: 0.7541 (ttp) cc_final: 0.7294 (ttp) REVERT: A 720 LYS cc_start: 0.7933 (ptmm) cc_final: 0.7629 (ptpp) REVERT: A 761 ILE cc_start: 0.8318 (mp) cc_final: 0.7605 (mp) REVERT: A 810 ILE cc_start: 0.8947 (mt) cc_final: 0.8650 (tt) REVERT: A 841 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7235 (mm-30) REVERT: A 844 THR cc_start: 0.8486 (m) cc_final: 0.8275 (m) REVERT: A 958 LYS cc_start: 0.8217 (mtpt) cc_final: 0.7842 (mtpp) REVERT: A 969 VAL cc_start: 0.8041 (m) cc_final: 0.7811 (t) REVERT: A 1002 MET cc_start: 0.7375 (mmt) cc_final: 0.7049 (mmt) REVERT: A 1011 TRP cc_start: 0.6936 (m100) cc_final: 0.6713 (m100) REVERT: A 1024 GLU cc_start: 0.8076 (pm20) cc_final: 0.7834 (pm20) outliers start: 3 outliers final: 2 residues processed: 213 average time/residue: 0.1131 time to fit residues: 29.7600 Evaluate side-chains 187 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 185 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 1017 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.0370 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 HIS A 442 ASN A 581 ASN ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN A 851 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.139657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.116749 restraints weight = 10689.264| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.68 r_work: 0.3417 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6555 Z= 0.149 Angle : 0.591 6.605 8932 Z= 0.305 Chirality : 0.042 0.152 999 Planarity : 0.004 0.040 1050 Dihedral : 11.362 146.769 1027 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.46 % Favored : 96.40 % Rotamer: Outliers : 5.13 % Allowed : 24.59 % Favored : 70.29 % 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 aren not related in a simple way. whole: 0.41 (0.32), residues: 722 helix: 1.18 (0.27), residues: 385 sheet: -0.69 (0.83), residues: 42 loop : -0.74 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 550 TYR 0.011 0.001 TYR A 415 PHE 0.019 0.002 PHE A 668 TRP 0.024 0.002 TRP A 799 HIS 0.010 0.001 HIS A 560 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6555) covalent geometry : angle 0.59052 ( 8932) hydrogen bonds : bond 0.04410 ( 298) hydrogen bonds : angle 4.60607 ( 842) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7780 (ptm) cc_final: 0.7369 (ptm) REVERT: A 422 LYS cc_start: 0.8360 (tttt) cc_final: 0.8025 (ttmt) REVERT: A 428 GLU cc_start: 0.6958 (tt0) cc_final: 0.6726 (tt0) REVERT: A 435 THR cc_start: 0.8475 (p) cc_final: 0.8094 (t) REVERT: A 444 GLU cc_start: 0.7526 (mp0) cc_final: 0.7242 (mp0) REVERT: A 457 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7467 (mt-10) REVERT: A 458 ILE cc_start: 0.8790 (mt) cc_final: 0.8587 (tt) REVERT: A 482 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.6730 (tp-100) REVERT: A 485 LYS cc_start: 0.8444 (tttp) cc_final: 0.8189 (tptm) REVERT: A 502 GLU cc_start: 0.7354 (tp30) cc_final: 0.6811 (tp30) REVERT: A 541 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7322 (mtmm) REVERT: A 618 ASN cc_start: 0.8376 (t0) cc_final: 0.8074 (t0) REVERT: A 625 MET cc_start: 0.7013 (tmm) cc_final: 0.6802 (tmm) REVERT: A 631 ARG cc_start: 0.8139 (ttm-80) cc_final: 0.7877 (ttp80) REVERT: A 677 ARG cc_start: 0.8096 (mtt90) cc_final: 0.7878 (mtt-85) REVERT: A 681 GLN cc_start: 0.7990 (mm110) cc_final: 0.7694 (mm110) REVERT: A 686 LYS cc_start: 0.8399 (ttmt) cc_final: 0.8138 (ttmm) REVERT: A 720 LYS cc_start: 0.8309 (ptmm) cc_final: 0.7983 (ptpp) REVERT: A 735 VAL cc_start: 0.5544 (p) cc_final: 0.4596 (m) REVERT: A 761 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8197 (mp) REVERT: A 765 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7214 (mtm-85) REVERT: A 776 ASP cc_start: 0.7549 (t0) cc_final: 0.7171 (t0) REVERT: A 777 VAL cc_start: 0.8790 (p) cc_final: 0.8561 (p) REVERT: A 783 GLU cc_start: 0.7519 (tp30) cc_final: 0.7231 (tp30) REVERT: A 810 ILE cc_start: 0.9047 (mt) cc_final: 0.8773 (tt) REVERT: A 841 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7350 (mm-30) REVERT: A 897 ASP cc_start: 0.7664 (p0) cc_final: 0.7456 (p0) REVERT: A 910 HIS cc_start: 0.6936 (OUTLIER) cc_final: 0.6573 (p90) REVERT: A 929 ASP cc_start: 0.6128 (OUTLIER) cc_final: 0.5749 (m-30) REVERT: A 936 CYS cc_start: 0.8241 (t) cc_final: 0.7933 (t) REVERT: A 964 ILE cc_start: 0.8294 (pt) cc_final: 0.8078 (pt) REVERT: A 1002 MET cc_start: 0.6985 (mmt) cc_final: 0.6668 (mmt) outliers start: 34 outliers final: 15 residues processed: 223 average time/residue: 0.0954 time to fit residues: 26.3814 Evaluate side-chains 206 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 HIS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 910 HIS Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1017 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 65 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 48 optimal weight: 0.0770 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.139050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.116459 restraints weight = 10541.971| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.68 r_work: 0.3392 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6555 Z= 0.139 Angle : 0.578 8.294 8932 Z= 0.296 Chirality : 0.042 0.142 999 Planarity : 0.004 0.036 1050 Dihedral : 11.318 146.029 1024 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.46 % Favored : 96.40 % Rotamer: Outliers : 4.98 % Allowed : 27.30 % Favored : 67.72 % 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 aren not related in a simple way. whole: 0.60 (0.32), residues: 722 helix: 1.43 (0.27), residues: 386 sheet: -0.76 (0.81), residues: 44 loop : -0.80 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 483 TYR 0.017 0.001 TYR A 484 PHE 0.011 0.001 PHE A 725 TRP 0.015 0.001 TRP A 940 HIS 0.005 0.001 HIS A 560 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 6555) covalent geometry : angle 0.57772 ( 8932) hydrogen bonds : bond 0.04009 ( 298) hydrogen bonds : angle 4.39997 ( 842) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: A 272 MET cc_start: 0.7820 (ptm) cc_final: 0.7384 (ptm) REVERT: A 422 LYS cc_start: 0.8311 (tttt) cc_final: 0.8022 (ttmt) REVERT: A 428 GLU cc_start: 0.7195 (tt0) cc_final: 0.6950 (tt0) REVERT: A 444 GLU cc_start: 0.7581 (mp0) cc_final: 0.7302 (mp0) REVERT: A 457 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7603 (mt-10) REVERT: A 483 ARG cc_start: 0.8518 (ptm160) cc_final: 0.8255 (tmm-80) REVERT: A 485 LYS cc_start: 0.8450 (tttp) cc_final: 0.8182 (tptm) REVERT: A 502 GLU cc_start: 0.7467 (tp30) cc_final: 0.6929 (tp30) REVERT: A 570 MET cc_start: 0.8350 (mmm) cc_final: 0.7521 (mmm) REVERT: A 591 ASP cc_start: 0.7839 (t0) cc_final: 0.7588 (t0) REVERT: A 618 ASN cc_start: 0.8428 (t0) cc_final: 0.8167 (t0) REVERT: A 619 LYS cc_start: 0.8924 (tptp) cc_final: 0.8691 (tptm) REVERT: A 625 MET cc_start: 0.6732 (tmm) cc_final: 0.6526 (tmm) REVERT: A 631 ARG cc_start: 0.8175 (ttm-80) cc_final: 0.7893 (ttp80) REVERT: A 677 ARG cc_start: 0.8219 (mtt90) cc_final: 0.7940 (mtt-85) REVERT: A 681 GLN cc_start: 0.8045 (mm110) cc_final: 0.7753 (mm110) REVERT: A 686 LYS cc_start: 0.8434 (ttmt) cc_final: 0.8154 (ttmm) REVERT: A 707 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.8302 (m-80) REVERT: A 735 VAL cc_start: 0.5573 (p) cc_final: 0.4687 (m) REVERT: A 761 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8163 (mp) REVERT: A 765 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7288 (mtm-85) REVERT: A 776 ASP cc_start: 0.7562 (t0) cc_final: 0.7163 (t0) REVERT: A 777 VAL cc_start: 0.8784 (p) cc_final: 0.8524 (p) REVERT: A 807 VAL cc_start: 0.8632 (m) cc_final: 0.8400 (p) REVERT: A 810 ILE cc_start: 0.9059 (mt) cc_final: 0.8785 (tt) REVERT: A 841 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7369 (mm-30) REVERT: A 846 LYS cc_start: 0.8606 (mttm) cc_final: 0.7996 (mttm) REVERT: A 883 VAL cc_start: 0.8234 (t) cc_final: 0.7748 (t) REVERT: A 910 HIS cc_start: 0.6919 (OUTLIER) cc_final: 0.6584 (p90) REVERT: A 929 ASP cc_start: 0.6159 (OUTLIER) cc_final: 0.5769 (m-30) REVERT: A 936 CYS cc_start: 0.8214 (t) cc_final: 0.7903 (t) REVERT: A 953 LEU cc_start: 0.7889 (tp) cc_final: 0.7557 (tp) REVERT: A 1002 MET cc_start: 0.6949 (mmt) cc_final: 0.6652 (mmt) outliers start: 33 outliers final: 15 residues processed: 212 average time/residue: 0.1062 time to fit residues: 27.8892 Evaluate side-chains 207 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 910 HIS Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 963 TRP Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1017 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 ASN ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.136661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.114231 restraints weight = 10578.165| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.71 r_work: 0.3344 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6555 Z= 0.200 Angle : 0.604 7.826 8932 Z= 0.316 Chirality : 0.045 0.152 999 Planarity : 0.004 0.039 1050 Dihedral : 11.273 146.740 1024 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.74 % Favored : 96.12 % Rotamer: Outliers : 4.98 % Allowed : 27.60 % Favored : 67.42 % 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 aren not related in a simple way. whole: 0.49 (0.32), residues: 722 helix: 1.40 (0.27), residues: 383 sheet: -0.91 (0.81), residues: 44 loop : -0.89 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 945 TYR 0.011 0.002 TYR A1061 PHE 0.019 0.002 PHE A 651 TRP 0.018 0.002 TRP A 940 HIS 0.005 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 6555) covalent geometry : angle 0.60419 ( 8932) hydrogen bonds : bond 0.04712 ( 298) hydrogen bonds : angle 4.52065 ( 842) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 272 MET cc_start: 0.7829 (ptm) cc_final: 0.7391 (ptm) REVERT: A 430 ASP cc_start: 0.7840 (m-30) cc_final: 0.7610 (m-30) REVERT: A 444 GLU cc_start: 0.7663 (mp0) cc_final: 0.7393 (mp0) REVERT: A 468 LYS cc_start: 0.8934 (mmmm) cc_final: 0.8670 (mtmm) REVERT: A 502 GLU cc_start: 0.7520 (tp30) cc_final: 0.7018 (tp30) REVERT: A 536 MET cc_start: 0.7773 (mtp) cc_final: 0.7564 (mtm) REVERT: A 555 ILE cc_start: 0.8191 (tp) cc_final: 0.7951 (tp) REVERT: A 570 MET cc_start: 0.8360 (mmm) cc_final: 0.7641 (mmm) REVERT: A 588 ARG cc_start: 0.8695 (mmm-85) cc_final: 0.8494 (mtp-110) REVERT: A 672 LEU cc_start: 0.9180 (tp) cc_final: 0.8919 (tt) REVERT: A 677 ARG cc_start: 0.8489 (mtt90) cc_final: 0.8060 (mtt-85) REVERT: A 681 GLN cc_start: 0.8196 (mm110) cc_final: 0.7847 (mm110) REVERT: A 735 VAL cc_start: 0.6403 (p) cc_final: 0.5592 (m) REVERT: A 764 LYS cc_start: 0.8044 (mmmm) cc_final: 0.7631 (mmmm) REVERT: A 765 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7626 (mtm-85) REVERT: A 768 TYR cc_start: 0.7963 (t80) cc_final: 0.7703 (t80) REVERT: A 802 ILE cc_start: 0.7422 (OUTLIER) cc_final: 0.6996 (mp) REVERT: A 807 VAL cc_start: 0.8605 (m) cc_final: 0.8370 (p) REVERT: A 810 ILE cc_start: 0.9044 (mt) cc_final: 0.8783 (tt) REVERT: A 834 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7587 (tmm) REVERT: A 836 PHE cc_start: 0.8399 (t80) cc_final: 0.8067 (t80) REVERT: A 841 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7405 (mm-30) REVERT: A 910 HIS cc_start: 0.7062 (OUTLIER) cc_final: 0.6691 (p90) REVERT: A 953 LEU cc_start: 0.7833 (tp) cc_final: 0.7447 (tp) REVERT: A 962 ARG cc_start: 0.8467 (ttp80) cc_final: 0.8104 (ttp80) REVERT: A 967 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8178 (pp) REVERT: A 1002 MET cc_start: 0.7003 (mmt) cc_final: 0.6652 (mmt) outliers start: 33 outliers final: 16 residues processed: 218 average time/residue: 0.0940 time to fit residues: 25.7291 Evaluate side-chains 219 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 198 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 659 GLN Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 834 MET Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 910 HIS Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1017 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 36 optimal weight: 0.6980 chunk 67 optimal weight: 0.0030 chunk 53 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 50.0000 chunk 62 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN A 851 GLN ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.138652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.115748 restraints weight = 10665.757| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.75 r_work: 0.3373 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6555 Z= 0.130 Angle : 0.572 7.575 8932 Z= 0.299 Chirality : 0.042 0.145 999 Planarity : 0.004 0.034 1050 Dihedral : 11.106 145.412 1024 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.74 % Favored : 96.12 % Rotamer: Outliers : 3.62 % Allowed : 30.47 % Favored : 65.91 % 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 aren not related in a simple way. whole: 0.51 (0.32), residues: 722 helix: 1.37 (0.27), residues: 392 sheet: -0.90 (0.81), residues: 44 loop : -0.88 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 945 TYR 0.008 0.001 TYR A 914 PHE 0.012 0.001 PHE A 781 TRP 0.018 0.001 TRP A 940 HIS 0.007 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 6555) covalent geometry : angle 0.57195 ( 8932) hydrogen bonds : bond 0.03811 ( 298) hydrogen bonds : angle 4.26181 ( 842) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 266 MET cc_start: 0.8149 (tpp) cc_final: 0.7920 (tpp) REVERT: A 272 MET cc_start: 0.7821 (ptm) cc_final: 0.7375 (ptm) REVERT: A 275 GLU cc_start: 0.6148 (OUTLIER) cc_final: 0.5782 (mp0) REVERT: A 428 GLU cc_start: 0.7280 (tt0) cc_final: 0.6753 (tt0) REVERT: A 430 ASP cc_start: 0.7827 (m-30) cc_final: 0.7618 (m-30) REVERT: A 444 GLU cc_start: 0.7619 (mp0) cc_final: 0.7349 (mp0) REVERT: A 468 LYS cc_start: 0.8924 (mmmm) cc_final: 0.8676 (mtmm) REVERT: A 502 GLU cc_start: 0.7508 (tp30) cc_final: 0.7237 (tp30) REVERT: A 555 ILE cc_start: 0.7981 (tp) cc_final: 0.7737 (tp) REVERT: A 570 MET cc_start: 0.8435 (mmm) cc_final: 0.7664 (mmm) REVERT: A 588 ARG cc_start: 0.8682 (mmm-85) cc_final: 0.8048 (mtp-110) REVERT: A 593 ASN cc_start: 0.8091 (t0) cc_final: 0.7654 (t0) REVERT: A 672 LEU cc_start: 0.9155 (tp) cc_final: 0.8876 (tt) REVERT: A 677 ARG cc_start: 0.8448 (mtt90) cc_final: 0.8201 (ttm-80) REVERT: A 681 GLN cc_start: 0.8197 (mm110) cc_final: 0.7852 (mm110) REVERT: A 707 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.7872 (m-80) REVERT: A 735 VAL cc_start: 0.6203 (p) cc_final: 0.5433 (m) REVERT: A 764 LYS cc_start: 0.7891 (mmmm) cc_final: 0.7630 (mmmt) REVERT: A 765 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7218 (mtm-85) REVERT: A 768 TYR cc_start: 0.7930 (t80) cc_final: 0.7711 (t80) REVERT: A 783 GLU cc_start: 0.7795 (tp30) cc_final: 0.7516 (tp30) REVERT: A 802 ILE cc_start: 0.7392 (OUTLIER) cc_final: 0.6987 (mp) REVERT: A 807 VAL cc_start: 0.8561 (m) cc_final: 0.8337 (p) REVERT: A 810 ILE cc_start: 0.9005 (mt) cc_final: 0.8765 (tt) REVERT: A 834 MET cc_start: 0.8089 (mmm) cc_final: 0.7516 (tmm) REVERT: A 836 PHE cc_start: 0.8342 (t80) cc_final: 0.8009 (t80) REVERT: A 841 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7400 (mm-30) REVERT: A 910 HIS cc_start: 0.6993 (OUTLIER) cc_final: 0.6640 (p90) REVERT: A 929 ASP cc_start: 0.6099 (OUTLIER) cc_final: 0.5793 (m-30) REVERT: A 953 LEU cc_start: 0.7572 (tp) cc_final: 0.7204 (tp) REVERT: A 962 ARG cc_start: 0.8421 (ttp80) cc_final: 0.8022 (ttp80) REVERT: A 984 THR cc_start: 0.8114 (m) cc_final: 0.7633 (t) REVERT: A 1002 MET cc_start: 0.6948 (mmt) cc_final: 0.6570 (mmt) outliers start: 24 outliers final: 14 residues processed: 199 average time/residue: 0.1107 time to fit residues: 27.5639 Evaluate side-chains 205 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 494 LYS Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 659 GLN Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 910 HIS Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 963 TRP Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1017 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 3.9990 chunk 27 optimal weight: 0.0970 chunk 17 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 46 optimal weight: 0.1980 chunk 59 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 0.2980 chunk 18 optimal weight: 0.8980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 ASN ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.140410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.117571 restraints weight = 10514.872| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.73 r_work: 0.3357 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6555 Z= 0.118 Angle : 0.569 7.807 8932 Z= 0.293 Chirality : 0.041 0.153 999 Planarity : 0.004 0.033 1050 Dihedral : 10.990 145.218 1024 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.46 % Favored : 96.40 % Rotamer: Outliers : 4.52 % Allowed : 30.02 % Favored : 65.46 % 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 aren not related in a simple way. whole: 0.63 (0.32), residues: 722 helix: 1.39 (0.27), residues: 384 sheet: -0.89 (0.79), residues: 44 loop : -0.63 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 483 TYR 0.008 0.001 TYR A 914 PHE 0.014 0.001 PHE A 741 TRP 0.019 0.001 TRP A 940 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6555) covalent geometry : angle 0.56911 ( 8932) hydrogen bonds : bond 0.03516 ( 298) hydrogen bonds : angle 4.17122 ( 842) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: A 266 MET cc_start: 0.8253 (tpp) cc_final: 0.7963 (tpp) REVERT: A 272 MET cc_start: 0.7822 (ptm) cc_final: 0.7373 (ptm) REVERT: A 275 GLU cc_start: 0.6095 (OUTLIER) cc_final: 0.5744 (mp0) REVERT: A 428 GLU cc_start: 0.7342 (tt0) cc_final: 0.6773 (tt0) REVERT: A 430 ASP cc_start: 0.7838 (m-30) cc_final: 0.7590 (m-30) REVERT: A 468 LYS cc_start: 0.8946 (mmmm) cc_final: 0.8687 (mtmm) REVERT: A 502 GLU cc_start: 0.7541 (tp30) cc_final: 0.7314 (tp30) REVERT: A 555 ILE cc_start: 0.7931 (tp) cc_final: 0.7648 (tp) REVERT: A 588 ARG cc_start: 0.8677 (mmm-85) cc_final: 0.8037 (mtp-110) REVERT: A 593 ASN cc_start: 0.8086 (t0) cc_final: 0.7623 (t0) REVERT: A 672 LEU cc_start: 0.9084 (tp) cc_final: 0.8790 (tt) REVERT: A 677 ARG cc_start: 0.8447 (mtt90) cc_final: 0.8207 (mtt-85) REVERT: A 735 VAL cc_start: 0.5934 (p) cc_final: 0.5196 (m) REVERT: A 739 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8208 (mt0) REVERT: A 764 LYS cc_start: 0.7899 (mmmm) cc_final: 0.7694 (mmmt) REVERT: A 783 GLU cc_start: 0.7822 (tp30) cc_final: 0.7613 (tp30) REVERT: A 807 VAL cc_start: 0.8547 (m) cc_final: 0.8276 (p) REVERT: A 810 ILE cc_start: 0.8969 (mt) cc_final: 0.8738 (tt) REVERT: A 834 MET cc_start: 0.8112 (mmm) cc_final: 0.7469 (tmm) REVERT: A 836 PHE cc_start: 0.8334 (t80) cc_final: 0.8065 (t80) REVERT: A 910 HIS cc_start: 0.6980 (OUTLIER) cc_final: 0.6669 (p90) REVERT: A 929 ASP cc_start: 0.6114 (OUTLIER) cc_final: 0.5774 (m-30) REVERT: A 962 ARG cc_start: 0.8464 (ttp80) cc_final: 0.8037 (ttp80) REVERT: A 984 THR cc_start: 0.8118 (m) cc_final: 0.7589 (t) REVERT: A 1002 MET cc_start: 0.6959 (mmt) cc_final: 0.6538 (mmt) outliers start: 30 outliers final: 20 residues processed: 205 average time/residue: 0.1026 time to fit residues: 26.3544 Evaluate side-chains 209 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 494 LYS Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 659 GLN Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 910 HIS Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 963 TRP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1017 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 53 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 72 optimal weight: 0.3980 chunk 57 optimal weight: 0.0970 chunk 59 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 ASN ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.139763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.117389 restraints weight = 10448.062| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.68 r_work: 0.3346 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6555 Z= 0.126 Angle : 0.594 8.615 8932 Z= 0.306 Chirality : 0.042 0.161 999 Planarity : 0.004 0.032 1050 Dihedral : 10.935 145.641 1024 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.60 % Favored : 96.26 % Rotamer: Outliers : 4.68 % Allowed : 30.77 % Favored : 64.56 % 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 aren not related in a simple way. whole: 0.61 (0.32), residues: 722 helix: 1.34 (0.27), residues: 382 sheet: -0.85 (0.79), residues: 44 loop : -0.58 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 945 TYR 0.007 0.001 TYR A 914 PHE 0.014 0.001 PHE A 781 TRP 0.022 0.001 TRP A 940 HIS 0.007 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 6555) covalent geometry : angle 0.59447 ( 8932) hydrogen bonds : bond 0.03595 ( 298) hydrogen bonds : angle 4.17965 ( 842) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.241 Fit side-chains REVERT: A 266 MET cc_start: 0.8237 (tpp) cc_final: 0.7943 (tpp) REVERT: A 272 MET cc_start: 0.7812 (ptm) cc_final: 0.7356 (ptm) REVERT: A 275 GLU cc_start: 0.6088 (OUTLIER) cc_final: 0.5754 (mp0) REVERT: A 428 GLU cc_start: 0.7357 (tt0) cc_final: 0.6787 (tt0) REVERT: A 430 ASP cc_start: 0.7823 (m-30) cc_final: 0.7556 (m-30) REVERT: A 468 LYS cc_start: 0.8926 (mmmm) cc_final: 0.8683 (mtmm) REVERT: A 555 ILE cc_start: 0.7976 (tp) cc_final: 0.7679 (tp) REVERT: A 588 ARG cc_start: 0.8669 (mmm-85) cc_final: 0.8036 (mtp-110) REVERT: A 593 ASN cc_start: 0.8103 (t0) cc_final: 0.7637 (t0) REVERT: A 672 LEU cc_start: 0.9104 (tp) cc_final: 0.8807 (tt) REVERT: A 677 ARG cc_start: 0.8455 (mtt90) cc_final: 0.8209 (mtt-85) REVERT: A 739 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8233 (mt0) REVERT: A 764 LYS cc_start: 0.8046 (mmmm) cc_final: 0.7677 (mmmm) REVERT: A 834 MET cc_start: 0.8105 (mmm) cc_final: 0.7426 (tmm) REVERT: A 836 PHE cc_start: 0.8344 (t80) cc_final: 0.8084 (t80) REVERT: A 846 LYS cc_start: 0.8589 (mttm) cc_final: 0.8044 (mttm) REVERT: A 913 ASN cc_start: 0.7482 (p0) cc_final: 0.6547 (p0) REVERT: A 929 ASP cc_start: 0.6081 (OUTLIER) cc_final: 0.5733 (m-30) REVERT: A 958 LYS cc_start: 0.8565 (mttm) cc_final: 0.8221 (mttp) REVERT: A 962 ARG cc_start: 0.8482 (ttp80) cc_final: 0.8085 (ttp80) REVERT: A 984 THR cc_start: 0.8119 (m) cc_final: 0.7599 (t) REVERT: A 1002 MET cc_start: 0.6981 (mmt) cc_final: 0.6574 (mmt) outliers start: 31 outliers final: 17 residues processed: 203 average time/residue: 0.1001 time to fit residues: 25.5087 Evaluate side-chains 198 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 659 GLN Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 963 TRP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1017 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 43 optimal weight: 0.0970 chunk 33 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 55 optimal weight: 0.0170 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.139482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.117272 restraints weight = 10451.089| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.64 r_work: 0.3363 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6555 Z= 0.121 Angle : 0.588 8.506 8932 Z= 0.302 Chirality : 0.042 0.166 999 Planarity : 0.004 0.032 1050 Dihedral : 10.873 145.698 1024 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.02 % Favored : 95.84 % Rotamer: Outliers : 4.22 % Allowed : 30.32 % Favored : 65.46 % 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 aren not related in a simple way. whole: 0.68 (0.32), residues: 722 helix: 1.37 (0.27), residues: 381 sheet: -0.86 (0.79), residues: 44 loop : -0.49 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 483 TYR 0.010 0.001 TYR A 914 PHE 0.015 0.001 PHE A 741 TRP 0.027 0.001 TRP A 940 HIS 0.004 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 6555) covalent geometry : angle 0.58750 ( 8932) hydrogen bonds : bond 0.03451 ( 298) hydrogen bonds : angle 4.16876 ( 842) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.161 Fit side-chains REVERT: A 266 MET cc_start: 0.8223 (tpp) cc_final: 0.7947 (tpp) REVERT: A 272 MET cc_start: 0.7757 (ptm) cc_final: 0.7292 (ptm) REVERT: A 275 GLU cc_start: 0.6061 (OUTLIER) cc_final: 0.5770 (mp0) REVERT: A 428 GLU cc_start: 0.7276 (tt0) cc_final: 0.6776 (tt0) REVERT: A 430 ASP cc_start: 0.7802 (m-30) cc_final: 0.7562 (m-30) REVERT: A 468 LYS cc_start: 0.8899 (mmmm) cc_final: 0.8684 (mtmm) REVERT: A 494 LYS cc_start: 0.8208 (mtpt) cc_final: 0.7947 (ptmt) REVERT: A 555 ILE cc_start: 0.7927 (tp) cc_final: 0.7626 (tp) REVERT: A 588 ARG cc_start: 0.8678 (mmm-85) cc_final: 0.8009 (mtp-110) REVERT: A 593 ASN cc_start: 0.8094 (t0) cc_final: 0.7651 (t0) REVERT: A 672 LEU cc_start: 0.9133 (tp) cc_final: 0.8831 (tt) REVERT: A 677 ARG cc_start: 0.8420 (mtt90) cc_final: 0.8177 (mtt-85) REVERT: A 739 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8261 (mt0) REVERT: A 834 MET cc_start: 0.8055 (mmm) cc_final: 0.7416 (tmm) REVERT: A 836 PHE cc_start: 0.8333 (t80) cc_final: 0.8122 (t80) REVERT: A 846 LYS cc_start: 0.8599 (mttm) cc_final: 0.8055 (mttm) REVERT: A 929 ASP cc_start: 0.5976 (OUTLIER) cc_final: 0.5633 (m-30) REVERT: A 962 ARG cc_start: 0.8445 (ttp80) cc_final: 0.8021 (ttp80) REVERT: A 1002 MET cc_start: 0.6921 (mmt) cc_final: 0.6505 (mmt) REVERT: A 1052 ARG cc_start: 0.8831 (mtp180) cc_final: 0.8612 (mtm180) outliers start: 28 outliers final: 19 residues processed: 203 average time/residue: 0.0915 time to fit residues: 23.0956 Evaluate side-chains 208 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 659 GLN Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 963 TRP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1017 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 22 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 chunk 2 optimal weight: 50.0000 chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN A 744 ASN ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.139764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.117624 restraints weight = 10673.222| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.70 r_work: 0.3369 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6555 Z= 0.130 Angle : 0.616 8.520 8932 Z= 0.315 Chirality : 0.042 0.168 999 Planarity : 0.004 0.034 1050 Dihedral : 10.836 145.788 1024 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.88 % Favored : 95.98 % Rotamer: Outliers : 3.62 % Allowed : 31.52 % Favored : 64.86 % 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 aren not related in a simple way. whole: 0.69 (0.32), residues: 722 helix: 1.41 (0.27), residues: 382 sheet: -0.84 (0.81), residues: 44 loop : -0.53 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 483 TYR 0.008 0.001 TYR A 891 PHE 0.013 0.001 PHE A 741 TRP 0.022 0.001 TRP A 940 HIS 0.004 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6555) covalent geometry : angle 0.61558 ( 8932) hydrogen bonds : bond 0.03562 ( 298) hydrogen bonds : angle 4.16959 ( 842) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.214 Fit side-chains REVERT: A 266 MET cc_start: 0.8166 (tpp) cc_final: 0.7928 (tpp) REVERT: A 272 MET cc_start: 0.7755 (ptm) cc_final: 0.7284 (ptm) REVERT: A 275 GLU cc_start: 0.6130 (OUTLIER) cc_final: 0.5890 (mp0) REVERT: A 428 GLU cc_start: 0.7282 (tt0) cc_final: 0.6751 (tt0) REVERT: A 430 ASP cc_start: 0.7823 (m-30) cc_final: 0.7547 (m-30) REVERT: A 468 LYS cc_start: 0.8904 (mmmm) cc_final: 0.8698 (mtmm) REVERT: A 494 LYS cc_start: 0.8205 (mtpt) cc_final: 0.7917 (ptmt) REVERT: A 555 ILE cc_start: 0.7937 (tp) cc_final: 0.7643 (tp) REVERT: A 588 ARG cc_start: 0.8699 (mmm-85) cc_final: 0.8044 (mtp-110) REVERT: A 672 LEU cc_start: 0.9160 (tp) cc_final: 0.8849 (tt) REVERT: A 677 ARG cc_start: 0.8439 (mtt90) cc_final: 0.8194 (mtt-85) REVERT: A 739 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8290 (mt0) REVERT: A 744 ASN cc_start: 0.7789 (OUTLIER) cc_final: 0.7544 (p0) REVERT: A 834 MET cc_start: 0.8069 (mmm) cc_final: 0.7433 (tmm) REVERT: A 836 PHE cc_start: 0.8331 (t80) cc_final: 0.8124 (t80) REVERT: A 846 LYS cc_start: 0.8607 (mttm) cc_final: 0.8065 (mttm) REVERT: A 929 ASP cc_start: 0.5991 (OUTLIER) cc_final: 0.5646 (m-30) REVERT: A 962 ARG cc_start: 0.8413 (ttp80) cc_final: 0.8032 (ttp80) REVERT: A 984 THR cc_start: 0.8080 (m) cc_final: 0.7621 (t) REVERT: A 1002 MET cc_start: 0.6959 (mmt) cc_final: 0.6551 (mmt) outliers start: 24 outliers final: 18 residues processed: 201 average time/residue: 0.0953 time to fit residues: 24.0463 Evaluate side-chains 200 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 659 GLN Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 963 TRP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1017 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 18 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN A 744 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.139408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.117063 restraints weight = 10417.238| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.69 r_work: 0.3334 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6555 Z= 0.139 Angle : 0.641 10.884 8932 Z= 0.324 Chirality : 0.043 0.171 999 Planarity : 0.004 0.033 1050 Dihedral : 10.832 145.819 1024 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.16 % Favored : 95.71 % Rotamer: Outliers : 3.62 % Allowed : 31.67 % Favored : 64.71 % 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 aren not related in a simple way. whole: 0.67 (0.32), residues: 722 helix: 1.38 (0.27), residues: 383 sheet: -0.87 (0.81), residues: 44 loop : -0.52 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 483 TYR 0.009 0.001 TYR A 743 PHE 0.015 0.001 PHE A 741 TRP 0.030 0.001 TRP A 940 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 6555) covalent geometry : angle 0.64050 ( 8932) hydrogen bonds : bond 0.03613 ( 298) hydrogen bonds : angle 4.15597 ( 842) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.237 Fit side-chains REVERT: A 266 MET cc_start: 0.8223 (tpp) cc_final: 0.7976 (tpp) REVERT: A 272 MET cc_start: 0.7788 (ptm) cc_final: 0.7316 (ptm) REVERT: A 275 GLU cc_start: 0.6144 (OUTLIER) cc_final: 0.5934 (mp0) REVERT: A 428 GLU cc_start: 0.7375 (tt0) cc_final: 0.6827 (tt0) REVERT: A 430 ASP cc_start: 0.7808 (m-30) cc_final: 0.7551 (m-30) REVERT: A 468 LYS cc_start: 0.8914 (mmmm) cc_final: 0.8700 (mtmm) REVERT: A 494 LYS cc_start: 0.8172 (mtpt) cc_final: 0.7879 (ttpp) REVERT: A 555 ILE cc_start: 0.7949 (tp) cc_final: 0.7649 (tp) REVERT: A 588 ARG cc_start: 0.8659 (mmm-85) cc_final: 0.7982 (mtp-110) REVERT: A 672 LEU cc_start: 0.9148 (tp) cc_final: 0.8862 (tt) REVERT: A 677 ARG cc_start: 0.8450 (mtt90) cc_final: 0.8206 (mtt-85) REVERT: A 739 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8318 (mt0) REVERT: A 744 ASN cc_start: 0.7826 (OUTLIER) cc_final: 0.7597 (p0) REVERT: A 834 MET cc_start: 0.8117 (mmm) cc_final: 0.7478 (tmm) REVERT: A 836 PHE cc_start: 0.8361 (t80) cc_final: 0.8152 (t80) REVERT: A 846 LYS cc_start: 0.8584 (mttm) cc_final: 0.8035 (mttm) REVERT: A 929 ASP cc_start: 0.5923 (OUTLIER) cc_final: 0.5582 (m-30) REVERT: A 974 ILE cc_start: 0.8248 (mm) cc_final: 0.8024 (mp) REVERT: A 984 THR cc_start: 0.8065 (m) cc_final: 0.7582 (t) REVERT: A 1002 MET cc_start: 0.7058 (mmt) cc_final: 0.6639 (mmt) outliers start: 24 outliers final: 18 residues processed: 188 average time/residue: 0.1020 time to fit residues: 24.0286 Evaluate side-chains 194 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 659 GLN Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 963 TRP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1017 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.136937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.114432 restraints weight = 10581.435| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.71 r_work: 0.3334 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6555 Z= 0.183 Angle : 0.666 9.699 8932 Z= 0.339 Chirality : 0.044 0.172 999 Planarity : 0.004 0.035 1050 Dihedral : 10.897 146.513 1024 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.88 % Favored : 95.98 % Rotamer: Outliers : 3.47 % Allowed : 32.13 % Favored : 64.40 % 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 aren not related in a simple way. whole: 0.55 (0.32), residues: 722 helix: 1.29 (0.27), residues: 388 sheet: -0.89 (0.82), residues: 44 loop : -0.64 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 483 TYR 0.011 0.001 TYR A 743 PHE 0.014 0.002 PHE A 741 TRP 0.031 0.002 TRP A 940 HIS 0.003 0.001 HIS A 585 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 6555) covalent geometry : angle 0.66563 ( 8932) hydrogen bonds : bond 0.04144 ( 298) hydrogen bonds : angle 4.26142 ( 842) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1603.50 seconds wall clock time: 28 minutes 12.15 seconds (1692.15 seconds total)