Starting phenix.real_space_refine on Tue Aug 4 21:03:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8sxt_40858/08_2026/8sxt_40858.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sxt_40858/08_2026/8sxt_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_2026/8sxt_40858.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sxt_40858/08_2026/8sxt_40858.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sxt_40858/08_2026/8sxt_40858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sxt_40858/08_2026/8sxt_40858.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8sxt_40858/08_2026/8sxt_40858.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8sxt_40858/08_2026/8sxt_40858.cif" } 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-2.2rc3-6140/lib/python3.11/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: {'RNAv2': 11} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 9} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {' U: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: 1.32, per 1000 atoms: 0.21 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: 0.39 Conformation dependent library (CDL) restraints added in 242.8 milliseconds 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: 0.56 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: 0.81 Time building geometry restraints manager: 0.49 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=" C4' DC B 11 " pdb=" C3' DC B 11 " ideal model delta sigma weight residual 1.529 1.511 0.018 1.00e-02 1.00e+04 3.12e+00 bond pdb=" C4' DT B 7 " pdb=" C3' DT B 7 " ideal model delta sigma weight residual 1.529 1.512 0.017 1.00e-02 1.00e+04 2.97e+00 bond pdb=" C2' DT B 7 " pdb=" C1' DT B 7 " ideal model delta sigma weight residual 1.518 1.535 -0.017 1.00e-02 1.00e+04 2.83e+00 ... (remaining 6550 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 8885 3.14 - 6.27: 43 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=" N3 DT B 6 " pdb=" C4 DT B 6 " pdb=" O4 DT B 6 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 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=" N3 DT B 8 " pdb=" C4 DT B 8 " pdb=" O4 DT B 8 " ideal model delta sigma weight residual 119.90 122.29 -2.39 6.00e-01 2.78e+00 1.59e+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 ... (remaining 8927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.59: 3710 29.59 - 59.17: 251 59.17 - 88.76: 20 88.76 - 118.34: 2 118.34 - 147.93: 1 Dihedral angle restraints: 3984 sinusoidal: 1836 harmonic: 2148 Sorted by residual: dihedral pdb=" C4' G C -1 " pdb=" C3' G C -1 " pdb=" C2' G C -1 " pdb=" C1' G C -1 " ideal model delta sinusoidal sigma weight residual 36.35 -36.06 72.41 1 3.10e+00 1.04e-01 6.97e+02 dihedral pdb=" O4' G C -1 " pdb=" C4' G C -1 " pdb=" C3' G C -1 " pdb=" C2' G C -1 " ideal model delta sinusoidal sigma weight residual -35.15 23.17 -58.31 1 4.00e+00 6.25e-02 2.85e+02 dihedral pdb=" O4' G C -1 " pdb=" C2' G C -1 " pdb=" C1' G C -1 " pdb=" C3' G C -1 " ideal model delta sinusoidal sigma weight residual -94.41 -37.60 -56.81 3 3.80e+00 6.93e-02 1.47e+02 ... (remaining 3981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 847 0.055 - 0.109: 128 0.109 - 0.164: 12 0.164 - 0.218: 0 0.218 - 0.273: 12 Chirality restraints: 999 Sorted by residual: chirality pdb=" C3' G C -1 " pdb=" C4' G C -1 " pdb=" O3' G C -1 " pdb=" C2' G C -1 " both_signs ideal model delta sigma weight residual False -2.50 -2.77 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C2' G C -1 " pdb=" C3' G C -1 " pdb=" O2' G C -1 " pdb=" C1' G C -1 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" P U C 7 " pdb=" OP1 U C 7 " pdb=" OP2 U C 7 " pdb=" O5' U C 7 " both_signs ideal model delta sigma weight residual True 2.17 -2.41 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (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: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.700 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:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 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= 0.166 Angle : 0.635 15.684 8932 Z= 0.385 Chirality : 0.046 0.273 999 Planarity : 0.003 0.043 1050 Dihedral : 18.097 147.928 2588 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 are 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/Z covalent geometry : bond 0.00288 / 0.17 ( 6555) covalent geometry : angle 0.63543 / 0.39 ( 8932) hydrogen bonds : bond 0.17166 / 14.91 ( 298) hydrogen bonds : angle 6.25034 / 5.34 ( 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 : 0.147 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: 0.0792 time to fit residues: 21.0602 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 : 0.177 ------------------------------------------------------------------------------- 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: 0.9980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3891 r_free = 0.3891 target = 0.139733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.117117 restraints weight = 10719.658| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.62 r_work: 0.3431 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6555 Z= 0.162 Angle : 0.690 14.092 8932 Z= 0.351 Chirality : 0.054 0.888 999 Planarity : 0.004 0.038 1050 Dihedral : 11.854 146.535 1019 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.88 % Favored : 95.98 % Rotamer: Outliers : 4.98 % Allowed : 25.19 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.32), residues: 722 helix: 1.19 (0.27), residues: 384 sheet: -0.84 (0.80), residues: 42 loop : -0.63 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 588 TYR 0.012 0.001 TYR A 415 PHE 0.019 0.002 PHE A 668 TRP 0.023 0.002 TRP A 799 HIS 0.009 0.001 HIS A 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 6555) covalent geometry : angle 0.69043 / 0.35 ( 8932) hydrogen bonds : bond 0.04926 / 4.39 ( 298) hydrogen bonds : angle 4.73666 / 3.88 ( 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 220 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7742 (ptm) cc_final: 0.7383 (ptm) REVERT: A 422 LYS cc_start: 0.8396 (tttt) cc_final: 0.7966 (ttmt) REVERT: A 428 GLU cc_start: 0.7150 (tt0) cc_final: 0.6824 (tt0) REVERT: A 444 GLU cc_start: 0.7585 (mp0) cc_final: 0.7284 (mp0) REVERT: A 457 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7471 (mt-10) REVERT: A 485 LYS cc_start: 0.8412 (tttp) cc_final: 0.8070 (tptm) REVERT: A 502 GLU cc_start: 0.7312 (tp30) cc_final: 0.6756 (tp30) REVERT: A 555 ILE cc_start: 0.7868 (tp) cc_final: 0.7571 (tp) REVERT: A 582 VAL cc_start: 0.8416 (m) cc_final: 0.8129 (p) REVERT: A 618 ASN cc_start: 0.8386 (t0) cc_final: 0.8087 (t0) REVERT: A 631 ARG cc_start: 0.8099 (ttm-80) cc_final: 0.7841 (ttp80) REVERT: A 644 ASN cc_start: 0.8088 (m-40) cc_final: 0.7618 (t0) REVERT: A 677 ARG cc_start: 0.8037 (mtt90) cc_final: 0.7821 (mtt-85) REVERT: A 681 GLN cc_start: 0.7955 (mm110) cc_final: 0.7682 (mm110) REVERT: A 686 LYS cc_start: 0.8248 (ttmt) cc_final: 0.7961 (ttmm) REVERT: A 720 LYS cc_start: 0.8223 (ptmm) cc_final: 0.7919 (ptpp) REVERT: A 735 VAL cc_start: 0.5386 (p) cc_final: 0.4490 (m) REVERT: A 761 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7949 (mp) REVERT: A 764 LYS cc_start: 0.7660 (mmmt) cc_final: 0.7447 (mmmm) REVERT: A 765 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7225 (mtm-85) REVERT: A 776 ASP cc_start: 0.7433 (t0) cc_final: 0.7086 (t0) REVERT: A 777 VAL cc_start: 0.8754 (p) cc_final: 0.8520 (p) REVERT: A 810 ILE cc_start: 0.9000 (mt) cc_final: 0.8743 (tt) REVERT: A 841 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7434 (mm-30) REVERT: A 846 LYS cc_start: 0.8571 (mttm) cc_final: 0.7982 (mttm) REVERT: A 922 LYS cc_start: 0.7898 (mmmt) cc_final: 0.7610 (mmmt) REVERT: A 929 ASP cc_start: 0.6099 (OUTLIER) cc_final: 0.5681 (m-30) REVERT: A 958 LYS cc_start: 0.8199 (mtpt) cc_final: 0.7981 (mtpp) REVERT: A 1002 MET cc_start: 0.7011 (mmt) cc_final: 0.6706 (mmt) outliers start: 33 outliers final: 13 residues processed: 206 average time/residue: 0.0801 time to fit residues: 20.7406 Evaluate side-chains 199 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.152 ------------------------------------------------------------------------------- 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 488 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 741 PHE 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 766 ILE Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1014 ILE 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: 3.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 37 optimal weight: 2.9990 chunk 48 optimal weight: 0.0020 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 ASN ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN A 851 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.140903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.118116 restraints weight = 10587.768| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.69 r_work: 0.3427 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2031 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= 0.138 Angle : 0.629 8.186 8932 Z= 0.326 Chirality : 0.049 0.582 999 Planarity : 0.004 0.036 1050 Dihedral : 11.478 146.148 1016 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.74 % Favored : 96.12 % Rotamer: Outliers : 3.92 % Allowed : 26.55 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.32), residues: 722 helix: 1.27 (0.27), residues: 383 sheet: -0.93 (0.76), residues: 44 loop : -0.60 (0.37), 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 0.012 0.001 PHE A 668 TRP 0.018 0.001 TRP A 937 HIS 0.010 0.002 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 6555) covalent geometry : angle 0.62945 / 0.33 ( 8932) hydrogen bonds : bond 0.04292 / 3.95 ( 298) hydrogen bonds : angle 4.52356 / 3.75 ( 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 218 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 272 MET cc_start: 0.7791 (ptm) cc_final: 0.7408 (ptm) REVERT: A 422 LYS cc_start: 0.8350 (tttt) cc_final: 0.7887 (ttmt) REVERT: A 428 GLU cc_start: 0.7274 (tt0) cc_final: 0.6932 (tt0) REVERT: A 444 GLU cc_start: 0.7543 (mp0) cc_final: 0.7259 (mp0) REVERT: A 485 LYS cc_start: 0.8439 (tttp) cc_final: 0.8131 (tptm) REVERT: A 502 GLU cc_start: 0.7345 (tp30) cc_final: 0.6800 (tp30) REVERT: A 582 VAL cc_start: 0.8435 (m) cc_final: 0.8201 (p) REVERT: A 602 GLU cc_start: 0.7050 (tt0) cc_final: 0.6847 (tt0) REVERT: A 618 ASN cc_start: 0.8385 (t0) cc_final: 0.8078 (t0) REVERT: A 619 LYS cc_start: 0.8831 (tptp) cc_final: 0.8578 (tptm) REVERT: A 631 ARG cc_start: 0.8101 (ttm-80) cc_final: 0.7840 (ttp80) REVERT: A 636 LYS cc_start: 0.8747 (ptpp) cc_final: 0.8469 (ptpp) REVERT: A 644 ASN cc_start: 0.8131 (m-40) cc_final: 0.7678 (t0) REVERT: A 677 ARG cc_start: 0.8147 (mtt90) cc_final: 0.7897 (mtt-85) REVERT: A 681 GLN cc_start: 0.7939 (mm110) cc_final: 0.7650 (mm110) REVERT: A 686 LYS cc_start: 0.8327 (ttmt) cc_final: 0.8023 (ttmm) REVERT: A 720 LYS cc_start: 0.8247 (ptmm) cc_final: 0.7911 (ptpp) REVERT: A 735 VAL cc_start: 0.5384 (p) cc_final: 0.4455 (m) REVERT: A 761 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.8001 (mt) REVERT: A 765 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7369 (mtm-85) REVERT: A 776 ASP cc_start: 0.7475 (t0) cc_final: 0.7129 (t0) REVERT: A 795 ASP cc_start: 0.7638 (t0) cc_final: 0.7388 (t70) REVERT: A 807 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8330 (p) REVERT: A 810 ILE cc_start: 0.9021 (mt) cc_final: 0.8752 (tt) REVERT: A 910 HIS cc_start: 0.6891 (OUTLIER) cc_final: 0.6557 (p90) REVERT: A 929 ASP cc_start: 0.6169 (OUTLIER) cc_final: 0.5754 (m-30) REVERT: A 964 ILE cc_start: 0.8166 (pt) cc_final: 0.7954 (pt) REVERT: A 1002 MET cc_start: 0.6946 (mmt) cc_final: 0.6617 (mmt) outliers start: 26 outliers final: 15 residues processed: 204 average time/residue: 0.0805 time to fit residues: 20.5607 Evaluate side-chains 200 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 564 VAL 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 807 VAL Chi-restraints excluded: chain A residue 817 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 8 optimal weight: 20.0000 chunk 35 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN A 851 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.137438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.115020 restraints weight = 10637.099| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.69 r_work: 0.3350 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6555 Z= 0.211 Angle : 0.684 8.336 8932 Z= 0.353 Chirality : 0.052 0.537 999 Planarity : 0.005 0.043 1050 Dihedral : 11.548 147.520 1016 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.60 % Favored : 96.26 % Rotamer: Outliers : 5.28 % Allowed : 24.74 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.32), residues: 722 helix: 1.21 (0.27), residues: 382 sheet: -1.13 (0.78), residues: 44 loop : -0.83 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 945 TYR 0.015 0.002 TYR A 743 PHE 0.016 0.002 PHE A 875 TRP 0.022 0.002 TRP A 937 HIS 0.014 0.003 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 ( 6555) covalent geometry : angle 0.68435 / 0.35 ( 8932) hydrogen bonds : bond 0.04757 / 4.32 ( 298) hydrogen bonds : angle 4.52132 / 3.65 ( 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 230 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: A 272 MET cc_start: 0.7834 (ptm) cc_final: 0.7422 (ptm) REVERT: A 422 LYS cc_start: 0.8353 (tttt) cc_final: 0.8042 (ttmt) REVERT: A 428 GLU cc_start: 0.7327 (tt0) cc_final: 0.7072 (tt0) REVERT: A 444 GLU cc_start: 0.7619 (mp0) cc_final: 0.7325 (mp0) REVERT: A 485 LYS cc_start: 0.8596 (tttp) cc_final: 0.8334 (tptm) REVERT: A 502 GLU cc_start: 0.7522 (tp30) cc_final: 0.6984 (tp30) REVERT: A 505 LEU cc_start: 0.8637 (mp) cc_final: 0.8386 (mp) REVERT: A 570 MET cc_start: 0.8307 (mmm) cc_final: 0.7570 (mmm) REVERT: A 582 VAL cc_start: 0.8566 (m) cc_final: 0.8349 (p) REVERT: A 591 ASP cc_start: 0.7960 (t0) cc_final: 0.7669 (t0) REVERT: A 602 GLU cc_start: 0.7256 (tt0) cc_final: 0.7007 (tt0) REVERT: A 618 ASN cc_start: 0.8448 (t0) cc_final: 0.8198 (t0) REVERT: A 619 LYS cc_start: 0.8922 (tptp) cc_final: 0.8700 (tptm) REVERT: A 677 ARG cc_start: 0.8353 (mtt90) cc_final: 0.8012 (mtt-85) REVERT: A 681 GLN cc_start: 0.8105 (mm110) cc_final: 0.7795 (mm110) REVERT: A 686 LYS cc_start: 0.8414 (ttmt) cc_final: 0.8138 (ttmm) REVERT: A 735 VAL cc_start: 0.5972 (p) cc_final: 0.5056 (m) REVERT: A 761 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8329 (mp) REVERT: A 765 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7548 (mtm-85) REVERT: A 776 ASP cc_start: 0.7597 (t0) cc_final: 0.7190 (t0) REVERT: A 795 ASP cc_start: 0.7862 (t0) cc_final: 0.7257 (t0) REVERT: A 807 VAL cc_start: 0.8653 (m) cc_final: 0.8403 (p) REVERT: A 810 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8786 (tt) REVERT: A 840 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8326 (tt) REVERT: A 846 LYS cc_start: 0.8646 (mttm) cc_final: 0.8068 (mttm) REVERT: A 910 HIS cc_start: 0.7035 (OUTLIER) cc_final: 0.6648 (p90) REVERT: A 929 ASP cc_start: 0.6207 (OUTLIER) cc_final: 0.5817 (m-30) REVERT: A 939 ASN cc_start: 0.8349 (t0) cc_final: 0.8122 (t0) REVERT: A 953 LEU cc_start: 0.7994 (tp) cc_final: 0.7585 (tp) REVERT: A 962 ARG cc_start: 0.8475 (ttp80) cc_final: 0.8039 (ttp80) REVERT: A 1002 MET cc_start: 0.7069 (mmt) cc_final: 0.6741 (mmt) outliers start: 35 outliers final: 19 residues processed: 211 average time/residue: 0.0729 time to fit residues: 19.4283 Evaluate side-chains 216 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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 447 GLU Chi-restraints excluded: chain A residue 458 ILE 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 614 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 699 LEU 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 810 ILE Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 840 LEU 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 964 ILE 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: 1.9990 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 50 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 ASN ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN A 851 GLN A 980 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.137036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.114523 restraints weight = 10783.907| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.68 r_work: 0.3343 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 6555 Z= 0.206 Angle : 0.651 8.065 8932 Z= 0.339 Chirality : 0.050 0.485 999 Planarity : 0.004 0.040 1050 Dihedral : 11.567 147.360 1016 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.74 % Favored : 96.12 % Rotamer: Outliers : 5.43 % Allowed : 26.70 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.32), residues: 722 helix: 1.24 (0.27), residues: 382 sheet: -0.91 (0.81), residues: 44 loop : -0.80 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 483 TYR 0.009 0.001 TYR A1054 PHE 0.012 0.002 PHE A 725 TRP 0.022 0.002 TRP A 799 HIS 0.009 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.21 ( 6555) covalent geometry : angle 0.65065 / 0.34 ( 8932) hydrogen bonds : bond 0.04661 / 4.26 ( 298) hydrogen bonds : angle 4.49980 / 3.67 ( 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 235 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7870 (ptm) cc_final: 0.7432 (ptm) REVERT: A 422 LYS cc_start: 0.8290 (tttt) cc_final: 0.8022 (ttmt) REVERT: A 428 GLU cc_start: 0.7372 (tt0) cc_final: 0.7138 (tt0) REVERT: A 430 ASP cc_start: 0.7892 (m-30) cc_final: 0.7654 (m-30) REVERT: A 444 GLU cc_start: 0.7580 (mp0) cc_final: 0.7293 (mp0) REVERT: A 502 GLU cc_start: 0.7561 (tp30) cc_final: 0.7051 (tp30) REVERT: A 505 LEU cc_start: 0.8676 (mp) cc_final: 0.8394 (mp) REVERT: A 555 ILE cc_start: 0.8154 (tp) cc_final: 0.7953 (tp) REVERT: A 570 MET cc_start: 0.8321 (mmm) cc_final: 0.7579 (mmm) REVERT: A 571 GLN cc_start: 0.8159 (mt0) cc_final: 0.7728 (mm-40) REVERT: A 588 ARG cc_start: 0.8682 (mmm-85) cc_final: 0.8000 (mtp-110) REVERT: A 591 ASP cc_start: 0.7995 (t0) cc_final: 0.7772 (t0) REVERT: A 602 GLU cc_start: 0.7286 (tt0) cc_final: 0.6998 (tt0) REVERT: A 618 ASN cc_start: 0.8487 (t0) cc_final: 0.8270 (t0) REVERT: A 672 LEU cc_start: 0.9118 (tp) cc_final: 0.8865 (tt) REVERT: A 677 ARG cc_start: 0.8381 (mtt90) cc_final: 0.8025 (mtt-85) REVERT: A 681 GLN cc_start: 0.8205 (mm110) cc_final: 0.7915 (mm110) REVERT: A 686 LYS cc_start: 0.8468 (ttmt) cc_final: 0.8211 (ttmm) REVERT: A 735 VAL cc_start: 0.6246 (p) cc_final: 0.5355 (m) REVERT: A 741 PHE cc_start: 0.8454 (m-10) cc_final: 0.8173 (m-10) REVERT: A 761 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8387 (mp) REVERT: A 765 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7547 (mtm-85) REVERT: A 776 ASP cc_start: 0.7620 (t0) cc_final: 0.7207 (t0) REVERT: A 807 VAL cc_start: 0.8600 (m) cc_final: 0.8371 (p) REVERT: A 810 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8773 (tt) REVERT: A 910 HIS cc_start: 0.6971 (OUTLIER) cc_final: 0.6574 (p90) REVERT: A 929 ASP cc_start: 0.6199 (OUTLIER) cc_final: 0.5891 (m-30) REVERT: A 953 LEU cc_start: 0.7876 (tp) cc_final: 0.7467 (tp) REVERT: A 962 ARG cc_start: 0.8470 (ttp80) cc_final: 0.8075 (ttp80) REVERT: A 984 THR cc_start: 0.7975 (p) cc_final: 0.7655 (t) REVERT: A 1002 MET cc_start: 0.7143 (mmt) cc_final: 0.6708 (mmt) outliers start: 36 outliers final: 24 residues processed: 213 average time/residue: 0.0743 time to fit residues: 20.0046 Evaluate side-chains 229 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 0.131 ------------------------------------------------------------------------------- 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 447 GLU Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 659 GLN Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 699 LEU 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 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 810 ILE Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 910 HIS Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1014 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: 5.9990 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 44 optimal weight: 0.0570 chunk 6 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3837 r_free = 0.3837 target = 0.138191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.115816 restraints weight = 10602.097| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.67 r_work: 0.3373 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6555 Z= 0.150 Angle : 0.613 7.569 8932 Z= 0.320 Chirality : 0.047 0.425 999 Planarity : 0.004 0.036 1050 Dihedral : 11.438 147.139 1016 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.19 % Favored : 96.68 % Rotamer: Outliers : 4.83 % Allowed : 29.71 % 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 are not related in a simple way. whole: 0.51 (0.32), residues: 722 helix: 1.34 (0.27), residues: 382 sheet: -0.93 (0.80), residues: 44 loop : -0.74 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 945 TYR 0.008 0.001 TYR A 914 PHE 0.010 0.001 PHE A 725 TRP 0.024 0.002 TRP A 799 HIS 0.009 0.002 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 6555) covalent geometry : angle 0.61335 / 0.32 ( 8932) hydrogen bonds : bond 0.04166 / 3.86 ( 298) hydrogen bonds : angle 4.37633 / 3.58 ( 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 226 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 272 MET cc_start: 0.7825 (ptm) cc_final: 0.7369 (ptm) REVERT: A 422 LYS cc_start: 0.8283 (tttt) cc_final: 0.8048 (ttmt) REVERT: A 430 ASP cc_start: 0.7858 (m-30) cc_final: 0.7609 (m-30) REVERT: A 444 GLU cc_start: 0.7565 (mp0) cc_final: 0.7277 (mp0) REVERT: A 487 GLU cc_start: 0.7667 (pm20) cc_final: 0.7333 (pm20) REVERT: A 494 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8030 (ptmt) REVERT: A 502 GLU cc_start: 0.7528 (tp30) cc_final: 0.7015 (tp30) REVERT: A 505 LEU cc_start: 0.8672 (mt) cc_final: 0.8400 (mp) REVERT: A 555 ILE cc_start: 0.8088 (tp) cc_final: 0.7844 (tp) REVERT: A 570 MET cc_start: 0.8330 (mmm) cc_final: 0.7563 (mmm) REVERT: A 571 GLN cc_start: 0.8147 (mt0) cc_final: 0.7738 (mm-40) REVERT: A 588 ARG cc_start: 0.8652 (mmm-85) cc_final: 0.7951 (mtp-110) REVERT: A 591 ASP cc_start: 0.8003 (t0) cc_final: 0.7758 (t0) REVERT: A 593 ASN cc_start: 0.8068 (t0) cc_final: 0.7643 (t0) REVERT: A 602 GLU cc_start: 0.7229 (tt0) cc_final: 0.6960 (tt0) REVERT: A 618 ASN cc_start: 0.8476 (t0) cc_final: 0.8245 (t0) REVERT: A 672 LEU cc_start: 0.9131 (tp) cc_final: 0.8877 (tt) REVERT: A 677 ARG cc_start: 0.8364 (mtt90) cc_final: 0.7991 (mtt-85) REVERT: A 681 GLN cc_start: 0.8216 (mm110) cc_final: 0.7910 (mm110) REVERT: A 686 LYS cc_start: 0.8451 (ttmt) cc_final: 0.8189 (ttmm) REVERT: A 707 TYR cc_start: 0.8687 (OUTLIER) cc_final: 0.8090 (m-80) REVERT: A 735 VAL cc_start: 0.6180 (p) cc_final: 0.5331 (m) REVERT: A 741 PHE cc_start: 0.8386 (m-10) cc_final: 0.8098 (m-10) REVERT: A 761 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8364 (mp) REVERT: A 776 ASP cc_start: 0.7638 (t0) cc_final: 0.7223 (t0) REVERT: A 792 ILE cc_start: 0.8702 (mm) cc_final: 0.8424 (mt) REVERT: A 807 VAL cc_start: 0.8585 (m) cc_final: 0.8348 (p) REVERT: A 810 ILE cc_start: 0.9036 (mt) cc_final: 0.8771 (tt) REVERT: A 834 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7682 (tmm) REVERT: A 841 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7150 (mm-30) REVERT: A 910 HIS cc_start: 0.6910 (OUTLIER) cc_final: 0.6527 (p90) REVERT: A 929 ASP cc_start: 0.6167 (OUTLIER) cc_final: 0.5844 (m-30) REVERT: A 953 LEU cc_start: 0.7777 (tp) cc_final: 0.7411 (tp) REVERT: A 962 ARG cc_start: 0.8444 (ttp80) cc_final: 0.8093 (ttp80) REVERT: A 984 THR cc_start: 0.7969 (p) cc_final: 0.7661 (t) REVERT: A 1002 MET cc_start: 0.6995 (mmt) cc_final: 0.6581 (mmt) REVERT: A 1037 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7618 (mt-10) outliers start: 32 outliers final: 21 residues processed: 206 average time/residue: 0.0760 time to fit residues: 19.6483 Evaluate side-chains 222 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 0.139 ------------------------------------------------------------------------------- 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 457 GLU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 494 LYS Chi-restraints excluded: chain A residue 495 LEU 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 707 TYR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 834 MET 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 967 LEU Chi-restraints excluded: chain A residue 976 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 53 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 72 optimal weight: 0.1980 chunk 57 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 63 optimal weight: 0.1980 chunk 11 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 581 ASN ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN A 980 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.138969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.116816 restraints weight = 10474.002| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.63 r_work: 0.3371 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6555 Z= 0.135 Angle : 0.608 7.966 8932 Z= 0.316 Chirality : 0.046 0.362 999 Planarity : 0.004 0.041 1050 Dihedral : 11.380 146.738 1016 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.46 % Favored : 96.40 % Rotamer: Outliers : 3.77 % Allowed : 31.37 % 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 are not related in a simple way. whole: 0.52 (0.32), residues: 722 helix: 1.40 (0.27), residues: 378 sheet: -0.85 (0.81), residues: 44 loop : -0.80 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 945 TYR 0.008 0.001 TYR A 891 PHE 0.010 0.001 PHE A 847 TRP 0.019 0.001 TRP A 940 HIS 0.007 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 6555) covalent geometry : angle 0.60839 / 0.32 ( 8932) hydrogen bonds : bond 0.03921 / 3.64 ( 298) hydrogen bonds : angle 4.28707 / 3.51 ( 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 215 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7812 (ptm) cc_final: 0.7344 (ptm) REVERT: A 422 LYS cc_start: 0.8281 (tttt) cc_final: 0.8049 (ttmt) REVERT: A 430 ASP cc_start: 0.7828 (m-30) cc_final: 0.7605 (m-30) REVERT: A 444 GLU cc_start: 0.7554 (mp0) cc_final: 0.7267 (mp0) REVERT: A 494 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8047 (ptmt) REVERT: A 502 GLU cc_start: 0.7522 (tp30) cc_final: 0.6997 (tp30) REVERT: A 505 LEU cc_start: 0.8696 (mt) cc_final: 0.8421 (mp) REVERT: A 555 ILE cc_start: 0.8056 (tp) cc_final: 0.7786 (tp) REVERT: A 570 MET cc_start: 0.8328 (mmm) cc_final: 0.7544 (mmm) REVERT: A 571 GLN cc_start: 0.8153 (mt0) cc_final: 0.7853 (mm-40) REVERT: A 588 ARG cc_start: 0.8662 (mmm-85) cc_final: 0.8438 (mtp-110) REVERT: A 591 ASP cc_start: 0.7998 (t0) cc_final: 0.7765 (t0) REVERT: A 593 ASN cc_start: 0.8058 (t0) cc_final: 0.7662 (t0) REVERT: A 602 GLU cc_start: 0.7167 (tt0) cc_final: 0.6902 (tt0) REVERT: A 618 ASN cc_start: 0.8478 (t0) cc_final: 0.8238 (t0) REVERT: A 672 LEU cc_start: 0.9114 (tp) cc_final: 0.8855 (tt) REVERT: A 677 ARG cc_start: 0.8373 (mtt90) cc_final: 0.7973 (mtt-85) REVERT: A 681 GLN cc_start: 0.8200 (mm110) cc_final: 0.7874 (mm110) REVERT: A 686 LYS cc_start: 0.8421 (ttmt) cc_final: 0.8149 (ttmm) REVERT: A 707 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.7921 (m-80) REVERT: A 735 VAL cc_start: 0.6091 (p) cc_final: 0.5274 (m) REVERT: A 741 PHE cc_start: 0.8322 (m-10) cc_final: 0.8006 (m-10) REVERT: A 761 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8310 (mp) REVERT: A 776 ASP cc_start: 0.7652 (t0) cc_final: 0.7224 (t0) REVERT: A 783 GLU cc_start: 0.7887 (tp30) cc_final: 0.7545 (tp30) REVERT: A 792 ILE cc_start: 0.8682 (mm) cc_final: 0.8437 (mt) REVERT: A 807 VAL cc_start: 0.8552 (m) cc_final: 0.8331 (p) REVERT: A 810 ILE cc_start: 0.9015 (mt) cc_final: 0.8770 (tt) REVERT: A 834 MET cc_start: 0.8161 (mmm) cc_final: 0.7613 (tmm) REVERT: A 841 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7243 (mm-30) REVERT: A 910 HIS cc_start: 0.6895 (OUTLIER) cc_final: 0.6549 (p90) REVERT: A 953 LEU cc_start: 0.7715 (tp) cc_final: 0.7348 (tp) REVERT: A 962 ARG cc_start: 0.8437 (ttp80) cc_final: 0.8059 (ttp80) REVERT: A 1002 MET cc_start: 0.6879 (mmt) cc_final: 0.6457 (mmt) REVERT: A 1037 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7636 (mt-10) outliers start: 25 outliers final: 18 residues processed: 200 average time/residue: 0.0780 time to fit residues: 19.6802 Evaluate side-chains 218 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 0.133 ------------------------------------------------------------------------------- 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 457 GLU Chi-restraints excluded: chain A residue 494 LYS Chi-restraints excluded: chain A residue 495 LEU 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 707 TYR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 910 HIS Chi-restraints excluded: chain A residue 961 SER 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: 1.9990 chunk 16 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 0.0040 chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 ASN A 581 ASN ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.137306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.114792 restraints weight = 10458.891| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.66 r_work: 0.3341 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3873 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= 0.143 Angle : 0.622 8.565 8932 Z= 0.323 Chirality : 0.046 0.320 999 Planarity : 0.004 0.046 1050 Dihedral : 11.333 146.844 1016 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.32 % Favored : 96.54 % Rotamer: Outliers : 4.83 % Allowed : 30.47 % 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 are not related in a simple way. whole: 0.53 (0.32), residues: 722 helix: 1.39 (0.27), residues: 378 sheet: -0.75 (0.82), residues: 44 loop : -0.80 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 945 TYR 0.008 0.001 TYR A 415 PHE 0.015 0.001 PHE A 781 TRP 0.023 0.001 TRP A 940 HIS 0.013 0.002 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 6555) covalent geometry : angle 0.62212 / 0.32 ( 8932) hydrogen bonds : bond 0.03944 / 3.66 ( 298) hydrogen bonds : angle 4.29561 / 3.60 ( 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 222 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 272 MET cc_start: 0.7803 (ptm) cc_final: 0.7273 (ptm) REVERT: A 422 LYS cc_start: 0.8262 (tttt) cc_final: 0.7978 (ttmt) REVERT: A 430 ASP cc_start: 0.7841 (m-30) cc_final: 0.7629 (m-30) REVERT: A 444 GLU cc_start: 0.7599 (mp0) cc_final: 0.7302 (mp0) REVERT: A 494 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8017 (ptmt) REVERT: A 502 GLU cc_start: 0.7577 (tp30) cc_final: 0.7045 (tp30) REVERT: A 505 LEU cc_start: 0.8733 (mt) cc_final: 0.8472 (mp) REVERT: A 555 ILE cc_start: 0.8072 (tp) cc_final: 0.7789 (tp) REVERT: A 570 MET cc_start: 0.8353 (mmm) cc_final: 0.7552 (mmm) REVERT: A 571 GLN cc_start: 0.8178 (mt0) cc_final: 0.7861 (mm-40) REVERT: A 588 ARG cc_start: 0.8702 (mmm-85) cc_final: 0.8017 (mtp-110) REVERT: A 591 ASP cc_start: 0.8001 (t0) cc_final: 0.7774 (t0) REVERT: A 593 ASN cc_start: 0.8073 (t0) cc_final: 0.7677 (t0) REVERT: A 602 GLU cc_start: 0.7176 (tt0) cc_final: 0.6899 (tt0) REVERT: A 618 ASN cc_start: 0.8499 (t0) cc_final: 0.8264 (t0) REVERT: A 631 ARG cc_start: 0.8184 (ttp80) cc_final: 0.7890 (ttm170) REVERT: A 672 LEU cc_start: 0.9110 (tp) cc_final: 0.8852 (tt) REVERT: A 677 ARG cc_start: 0.8411 (mtt90) cc_final: 0.8001 (mtt-85) REVERT: A 681 GLN cc_start: 0.8211 (mm110) cc_final: 0.7877 (mm110) REVERT: A 707 TYR cc_start: 0.8673 (OUTLIER) cc_final: 0.7849 (m-80) REVERT: A 735 VAL cc_start: 0.6155 (p) cc_final: 0.5382 (m) REVERT: A 741 PHE cc_start: 0.8295 (m-10) cc_final: 0.7927 (m-10) REVERT: A 760 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8465 (p) REVERT: A 761 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8317 (mp) REVERT: A 765 ARG cc_start: 0.7789 (mtm-85) cc_final: 0.7467 (mpp80) REVERT: A 776 ASP cc_start: 0.7653 (t0) cc_final: 0.7234 (t0) REVERT: A 783 GLU cc_start: 0.7944 (tp30) cc_final: 0.7484 (tp30) REVERT: A 792 ILE cc_start: 0.8662 (mm) cc_final: 0.8435 (mt) REVERT: A 807 VAL cc_start: 0.8555 (m) cc_final: 0.8288 (p) REVERT: A 810 ILE cc_start: 0.9006 (mt) cc_final: 0.8761 (tt) REVERT: A 834 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7610 (tmm) REVERT: A 841 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7299 (mm-30) REVERT: A 910 HIS cc_start: 0.6947 (OUTLIER) cc_final: 0.6595 (p90) REVERT: A 929 ASP cc_start: 0.6111 (OUTLIER) cc_final: 0.5774 (m-30) REVERT: A 953 LEU cc_start: 0.7685 (tp) cc_final: 0.7324 (tp) REVERT: A 962 ARG cc_start: 0.8463 (ttp80) cc_final: 0.8082 (ttp80) REVERT: A 984 THR cc_start: 0.7977 (p) cc_final: 0.7650 (t) REVERT: A 1002 MET cc_start: 0.6938 (mmt) cc_final: 0.6521 (mmt) outliers start: 32 outliers final: 20 residues processed: 204 average time/residue: 0.0842 time to fit residues: 21.8351 Evaluate side-chains 222 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 457 GLU Chi-restraints excluded: chain A residue 494 LYS Chi-restraints excluded: chain A residue 495 LEU 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 659 GLN Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 761 ILE 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 817 ILE Chi-restraints excluded: chain A residue 834 MET 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 22 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 2 optimal weight: 50.0000 chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 66 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 56 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 581 ASN ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN A 744 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.138079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.115204 restraints weight = 10659.474| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.72 r_work: 0.3366 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4029 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= 0.136 Angle : 0.615 8.758 8932 Z= 0.319 Chirality : 0.046 0.278 999 Planarity : 0.004 0.046 1050 Dihedral : 11.311 147.112 1016 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.19 % Favored : 96.68 % Rotamer: Outliers : 4.07 % Allowed : 30.62 % Favored : 65.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.32), residues: 722 helix: 1.41 (0.27), residues: 377 sheet: -0.81 (0.81), residues: 44 loop : -0.75 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 945 TYR 0.008 0.001 TYR A 914 PHE 0.013 0.001 PHE A 781 TRP 0.032 0.002 TRP A 940 HIS 0.006 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 6555) covalent geometry : angle 0.61545 / 0.32 ( 8932) hydrogen bonds : bond 0.03797 / 3.52 ( 298) hydrogen bonds : angle 4.23673 / 3.51 ( 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 219 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 272 MET cc_start: 0.7741 (ptm) cc_final: 0.7327 (ptm) REVERT: A 422 LYS cc_start: 0.8315 (tttt) cc_final: 0.7947 (ttmt) REVERT: A 430 ASP cc_start: 0.7831 (m-30) cc_final: 0.7598 (m-30) REVERT: A 444 GLU cc_start: 0.7593 (mp0) cc_final: 0.7297 (mp0) REVERT: A 494 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7958 (ptmt) REVERT: A 497 GLN cc_start: 0.8028 (mt0) cc_final: 0.7823 (mt0) REVERT: A 502 GLU cc_start: 0.7572 (tp30) cc_final: 0.7269 (tp30) REVERT: A 505 LEU cc_start: 0.8727 (mt) cc_final: 0.8494 (mp) REVERT: A 555 ILE cc_start: 0.8048 (tp) cc_final: 0.7771 (tp) REVERT: A 570 MET cc_start: 0.8339 (mmm) cc_final: 0.7544 (mmm) REVERT: A 571 GLN cc_start: 0.8192 (mt0) cc_final: 0.7962 (mm-40) REVERT: A 588 ARG cc_start: 0.8691 (mmm-85) cc_final: 0.7995 (mtp-110) REVERT: A 591 ASP cc_start: 0.8032 (t0) cc_final: 0.7822 (t0) REVERT: A 593 ASN cc_start: 0.8075 (t0) cc_final: 0.7611 (t0) REVERT: A 602 GLU cc_start: 0.7159 (tt0) cc_final: 0.6883 (tt0) REVERT: A 618 ASN cc_start: 0.8505 (t0) cc_final: 0.8273 (t0) REVERT: A 631 ARG cc_start: 0.8167 (ttp80) cc_final: 0.7878 (ttm170) REVERT: A 672 LEU cc_start: 0.9117 (tp) cc_final: 0.8843 (tt) REVERT: A 677 ARG cc_start: 0.8434 (mtt90) cc_final: 0.8021 (mtt-85) REVERT: A 681 GLN cc_start: 0.8212 (mm110) cc_final: 0.7880 (mm110) REVERT: A 735 VAL cc_start: 0.6077 (p) cc_final: 0.5325 (m) REVERT: A 741 PHE cc_start: 0.8219 (m-10) cc_final: 0.7818 (m-10) REVERT: A 760 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8480 (p) REVERT: A 765 ARG cc_start: 0.7877 (mtm-85) cc_final: 0.7107 (mtm-85) REVERT: A 776 ASP cc_start: 0.7640 (t0) cc_final: 0.7210 (t0) REVERT: A 783 GLU cc_start: 0.7955 (tp30) cc_final: 0.7574 (tp30) REVERT: A 807 VAL cc_start: 0.8543 (m) cc_final: 0.8270 (p) REVERT: A 810 ILE cc_start: 0.8998 (mt) cc_final: 0.8769 (tt) REVERT: A 834 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7615 (tmm) REVERT: A 841 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7288 (mm-30) REVERT: A 846 LYS cc_start: 0.8579 (mttm) cc_final: 0.8035 (mttm) REVERT: A 910 HIS cc_start: 0.6941 (OUTLIER) cc_final: 0.6603 (p90) REVERT: A 929 ASP cc_start: 0.6053 (OUTLIER) cc_final: 0.5692 (m-30) REVERT: A 945 ARG cc_start: 0.7794 (ttm-80) cc_final: 0.7593 (ttm-80) REVERT: A 953 LEU cc_start: 0.7639 (tp) cc_final: 0.7277 (tp) REVERT: A 962 ARG cc_start: 0.8469 (ttp80) cc_final: 0.8104 (ttp80) REVERT: A 1002 MET cc_start: 0.7000 (mmt) cc_final: 0.6592 (mmt) outliers start: 27 outliers final: 18 residues processed: 205 average time/residue: 0.0827 time to fit residues: 21.4348 Evaluate side-chains 217 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 0.149 ------------------------------------------------------------------------------- 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 494 LYS Chi-restraints excluded: chain A residue 495 LEU 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 659 GLN Chi-restraints excluded: chain A residue 707 TYR 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 817 ILE Chi-restraints excluded: chain A residue 834 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 18 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3837 r_free = 0.3837 target = 0.137951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.115388 restraints weight = 10402.751| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.64 r_work: 0.3376 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6555 Z= 0.145 Angle : 0.647 11.547 8932 Z= 0.332 Chirality : 0.046 0.262 999 Planarity : 0.004 0.047 1050 Dihedral : 11.297 147.328 1016 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.19 % Favored : 96.68 % Rotamer: Outliers : 3.47 % Allowed : 31.07 % 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 are not related in a simple way. whole: 0.53 (0.32), residues: 722 helix: 1.39 (0.27), residues: 378 sheet: -0.81 (0.81), residues: 44 loop : -0.78 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 945 TYR 0.010 0.001 TYR A 914 PHE 0.013 0.001 PHE A 781 TRP 0.036 0.002 TRP A 940 HIS 0.006 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 ( 6555) covalent geometry : angle 0.64731 / 0.33 ( 8932) hydrogen bonds : bond 0.03837 / 3.55 ( 298) hydrogen bonds : angle 4.25363 / 3.48 ( 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 216 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: A 272 MET cc_start: 0.7755 (ptm) cc_final: 0.7313 (ptm) REVERT: A 422 LYS cc_start: 0.8289 (tttt) cc_final: 0.7951 (ttmt) REVERT: A 430 ASP cc_start: 0.7833 (m-30) cc_final: 0.7595 (m-30) REVERT: A 444 GLU cc_start: 0.7554 (mp0) cc_final: 0.7268 (mp0) REVERT: A 494 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7936 (ptmt) REVERT: A 502 GLU cc_start: 0.7549 (tp30) cc_final: 0.7275 (tp30) REVERT: A 505 LEU cc_start: 0.8733 (mt) cc_final: 0.8500 (mp) REVERT: A 555 ILE cc_start: 0.8065 (tp) cc_final: 0.7782 (tp) REVERT: A 570 MET cc_start: 0.8327 (mmm) cc_final: 0.7517 (mmm) REVERT: A 588 ARG cc_start: 0.8678 (mmm-85) cc_final: 0.7977 (mtp-110) REVERT: A 593 ASN cc_start: 0.8069 (t0) cc_final: 0.7598 (t0) REVERT: A 602 GLU cc_start: 0.7124 (tt0) cc_final: 0.6850 (tt0) REVERT: A 618 ASN cc_start: 0.8473 (t0) cc_final: 0.8249 (t0) REVERT: A 672 LEU cc_start: 0.9116 (tp) cc_final: 0.8840 (tt) REVERT: A 677 ARG cc_start: 0.8445 (mtt90) cc_final: 0.8160 (mtt-85) REVERT: A 681 GLN cc_start: 0.8196 (mm110) cc_final: 0.7864 (mm110) REVERT: A 735 VAL cc_start: 0.6030 (p) cc_final: 0.5282 (m) REVERT: A 741 PHE cc_start: 0.8171 (m-10) cc_final: 0.7787 (m-10) REVERT: A 760 THR cc_start: 0.8858 (OUTLIER) cc_final: 0.8493 (p) REVERT: A 765 ARG cc_start: 0.7868 (mtm-85) cc_final: 0.7102 (mtm-85) REVERT: A 776 ASP cc_start: 0.7603 (t0) cc_final: 0.7178 (t0) REVERT: A 783 GLU cc_start: 0.7925 (tp30) cc_final: 0.7592 (tp30) REVERT: A 807 VAL cc_start: 0.8553 (m) cc_final: 0.8276 (p) REVERT: A 810 ILE cc_start: 0.8996 (mt) cc_final: 0.8770 (tt) REVERT: A 834 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7575 (tmm) REVERT: A 841 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7247 (mm-30) REVERT: A 846 LYS cc_start: 0.8575 (mttm) cc_final: 0.8013 (mttm) REVERT: A 910 HIS cc_start: 0.6907 (OUTLIER) cc_final: 0.6566 (p90) REVERT: A 929 ASP cc_start: 0.6075 (OUTLIER) cc_final: 0.5731 (m-30) REVERT: A 953 LEU cc_start: 0.7582 (tp) cc_final: 0.7238 (tp) REVERT: A 958 LYS cc_start: 0.8443 (mttm) cc_final: 0.8185 (mttp) REVERT: A 962 ARG cc_start: 0.8454 (ttp80) cc_final: 0.8082 (ttp80) REVERT: A 984 THR cc_start: 0.8072 (m) cc_final: 0.7587 (t) REVERT: A 1002 MET cc_start: 0.6990 (mmt) cc_final: 0.6610 (mmt) outliers start: 23 outliers final: 18 residues processed: 205 average time/residue: 0.0815 time to fit residues: 21.1007 Evaluate side-chains 212 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 494 LYS Chi-restraints excluded: chain A residue 495 LEU 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 659 GLN Chi-restraints excluded: chain A residue 707 TYR 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 817 ILE Chi-restraints excluded: chain A residue 834 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3830 r_free = 0.3830 target = 0.137467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.114537 restraints weight = 10551.255| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.71 r_work: 0.3330 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6555 Z= 0.148 Angle : 0.643 10.159 8932 Z= 0.331 Chirality : 0.046 0.247 999 Planarity : 0.004 0.048 1050 Dihedral : 11.303 147.576 1016 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.19 % Favored : 96.68 % Rotamer: Outliers : 3.47 % Allowed : 32.28 % Favored : 64.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.32), residues: 722 helix: 1.41 (0.27), residues: 376 sheet: -0.79 (0.81), residues: 44 loop : -0.82 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 945 TYR 0.009 0.001 TYR A 914 PHE 0.017 0.001 PHE A 574 TRP 0.042 0.002 TRP A 940 HIS 0.006 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 6555) covalent geometry : angle 0.64317 / 0.33 ( 8932) hydrogen bonds : bond 0.03861 / 3.54 ( 298) hydrogen bonds : angle 4.25732 / 3.47 ( 842) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1265.80 seconds wall clock time: 22 minutes 22.41 seconds (1342.41 seconds total)