Starting phenix.real_space_refine on Thu Jul 2 20:41:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wb0_32391/07_2026/7wb0_32391.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wb0_32391/07_2026/7wb0_32391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wb0_32391/07_2026/7wb0_32391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wb0_32391/07_2026/7wb0_32391.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wb0_32391/07_2026/7wb0_32391.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wb0_32391/07_2026/7wb0_32391.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wb0_32391/07_2026/7wb0_32391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wb0_32391/07_2026/7wb0_32391.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.054 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: 5 Type Number sf(0) Gaussians P 175 5.49 5 S 24 5.16 5 C 5765 2.51 5 N 1804 2.21 5 O 2328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10096 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 674 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "C" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 547 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "D" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2446 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 8, 'rna3p_pur': 55, 'rna3p_pyr': 47} Link IDs: {'rna2p': 13, 'rna3p': 101} Chain breaks: 1 Chain: "A" Number of atoms: 6429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 6429 Classifications: {'peptide': 797} Link IDs: {'PTRANS': 35, 'TRANS': 761} Chain breaks: 4 Time building chain proxies: 1.96, per 1000 atoms: 0.19 Number of scatterers: 10096 At special positions: 0 Unit cell: (104.34, 141, 125.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 175 15.00 O 2328 8.00 N 1804 7.00 C 5765 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 810 " - pdb=" SG CYS A 912 " distance=2.03 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: 0.76 Conformation dependent library (CDL) restraints added in 146.1 milliseconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 10 sheets defined 40.8% alpha, 18.4% beta 55 base pairs and 86 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 6 through 17 Processing helix chain 'A' and resid 38 through 47 Processing helix chain 'A' and resid 60 through 92 Processing helix chain 'A' and resid 92 through 100 removed outlier: 3.618A pdb=" N LEU A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 201 removed outlier: 3.533A pdb=" N HIS A 200 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 221 through 272 removed outlier: 3.662A pdb=" N VAL A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 250 " --> pdb=" O ASP A 246 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 309 Processing helix chain 'A' and resid 589 through 596 Processing helix chain 'A' and resid 647 through 650 removed outlier: 3.590A pdb=" N ILE A 650 " --> pdb=" O SER A 647 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 647 through 650' Processing helix chain 'A' and resid 697 through 717 removed outlier: 3.645A pdb=" N LYS A 701 " --> pdb=" O SER A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 724 Processing helix chain 'A' and resid 725 through 750 Processing helix chain 'A' and resid 770 through 774 removed outlier: 3.539A pdb=" N ARG A 774 " --> pdb=" O MET A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 790 removed outlier: 3.998A pdb=" N GLU A 790 " --> pdb=" O LYS A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 797 Processing helix chain 'A' and resid 821 through 829 removed outlier: 3.681A pdb=" N VAL A 825 " --> pdb=" O ASP A 821 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS A 828 " --> pdb=" O ARG A 824 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 829 " --> pdb=" O VAL A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 875 Processing helix chain 'A' and resid 881 through 885 removed outlier: 3.596A pdb=" N SER A 884 " --> pdb=" O ASP A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 898 Processing helix chain 'A' and resid 921 through 936 removed outlier: 3.569A pdb=" N ALA A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 951 removed outlier: 3.649A pdb=" N LYS A 942 " --> pdb=" O SER A 938 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A 950 " --> pdb=" O THR A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 973 removed outlier: 3.708A pdb=" N VAL A 959 " --> pdb=" O LYS A 955 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 502 through 506 removed outlier: 3.928A pdb=" N GLY A 614 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LEU A 611 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLU A 640 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN A 613 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU A 633 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 115 removed outlier: 3.988A pdb=" N ILE A 114 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE A 128 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 115 removed outlier: 3.988A pdb=" N ILE A 114 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 10.536A pdb=" N THR A 153 " --> pdb=" O PRO A 172 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR A 155 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 543 through 545 removed outlier: 3.671A pdb=" N LYS A 544 " --> pdb=" O GLU A 571 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 571 " --> pdb=" O LYS A 544 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE A 556 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N VAL A 559 " --> pdb=" O PHE A 517 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE A 517 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ASN A 561 " --> pdb=" O CYS A 515 " (cutoff:3.500A) removed outlier: 12.726A pdb=" N CYS A 515 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 516 " --> pdb=" O ILE A 532 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 691 through 694 removed outlier: 3.663A pdb=" N ALA A 666 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN A 654 " --> pdb=" O MET A 752 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ILE A 754 " --> pdb=" O ASN A 654 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE A 656 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ALA A 756 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 9.276A pdb=" N ILE A 658 " --> pdb=" O ALA A 756 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N THR A 801 " --> pdb=" O LEU A 753 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE A 755 " --> pdb=" O THR A 801 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 682 Processing sheet with id=AA8, first strand: chain 'A' and resid 831 through 832 removed outlier: 3.551A pdb=" N THR A 838 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 850 through 855 removed outlier: 3.583A pdb=" N TYR A 853 " --> pdb=" O VAL A 862 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 862 " --> pdb=" O TYR A 853 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 909 through 911 298 hydrogen bonds defined for protein. 849 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 137 hydrogen bonds 266 hydrogen bond angles 0 basepair planarities 55 basepair parallelities 86 stacking parallelities Total time for adding SS restraints: 2.30 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2062 1.33 - 1.45: 3183 1.45 - 1.57: 5025 1.57 - 1.69: 346 1.69 - 1.81: 36 Bond restraints: 10652 Sorted by residual: bond pdb=" C3' DG B 30 " pdb=" C2' DG B 30 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DG B 12 " pdb=" C2' DG B 12 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.92e+00 bond pdb=" C3' DT C 14 " pdb=" C2' DT C 14 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.73e+00 bond pdb=" C3' DA C 10 " pdb=" C2' DA C 10 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.75e+00 bond pdb=" C1' DC C 23 " pdb=" N1 DC C 23 " ideal model delta sigma weight residual 1.468 1.507 -0.039 1.40e-02 5.10e+03 7.61e+00 ... (remaining 10647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 14882 2.09 - 4.18: 274 4.18 - 6.27: 16 6.27 - 8.35: 2 8.35 - 10.44: 1 Bond angle restraints: 15175 Sorted by residual: angle pdb=" N3 DT B 11 " pdb=" C4 DT B 11 " pdb=" O4 DT B 11 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" O4' DT C 7 " pdb=" C4' DT C 7 " pdb=" C3' DT C 7 " ideal model delta sigma weight residual 106.00 103.46 2.54 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT B 26 " pdb=" C4 DT B 26 " pdb=" O4 DT B 26 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT B 2 " pdb=" C4 DT B 2 " pdb=" O4 DT B 2 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT B 3 " pdb=" C4 DT B 3 " pdb=" O4 DT B 3 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 ... (remaining 15170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.54: 5549 29.54 - 59.07: 459 59.07 - 88.61: 42 88.61 - 118.14: 2 118.14 - 147.68: 1 Dihedral angle restraints: 6053 sinusoidal: 3727 harmonic: 2326 Sorted by residual: dihedral pdb=" O4' U D 17 " pdb=" C1' U D 17 " pdb=" N1 U D 17 " pdb=" C2 U D 17 " ideal model delta sinusoidal sigma weight residual 232.00 84.32 147.68 1 1.70e+01 3.46e-03 6.13e+01 dihedral pdb=" CA HIS A 903 " pdb=" C HIS A 903 " pdb=" N ARG A 904 " pdb=" CA ARG A 904 " ideal model delta harmonic sigma weight residual -180.00 -160.13 -19.87 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA PRO A 333 " pdb=" C PRO A 333 " pdb=" N LEU A 334 " pdb=" CA LEU A 334 " ideal model delta harmonic sigma weight residual 180.00 160.71 19.29 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 6050 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1275 0.033 - 0.067: 355 0.067 - 0.100: 107 0.100 - 0.133: 39 0.133 - 0.166: 2 Chirality restraints: 1778 Sorted by residual: chirality pdb=" CB THR A 953 " pdb=" CA THR A 953 " pdb=" OG1 THR A 953 " pdb=" CG2 THR A 953 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CB ILE A 114 " pdb=" CA ILE A 114 " pdb=" CG1 ILE A 114 " pdb=" CG2 ILE A 114 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.78e-01 chirality pdb=" CA VAL A 667 " pdb=" N VAL A 667 " pdb=" C VAL A 667 " pdb=" CB VAL A 667 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 1775 not shown) Planarity restraints: 1303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 889 " 0.164 9.50e-02 1.11e+02 7.37e-02 3.41e+00 pdb=" NE ARG A 889 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 889 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 889 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 889 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U D 20 " 0.020 2.00e-02 2.50e+03 1.04e-02 2.44e+00 pdb=" N1 U D 20 " -0.022 2.00e-02 2.50e+03 pdb=" C2 U D 20 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U D 20 " -0.001 2.00e-02 2.50e+03 pdb=" N3 U D 20 " 0.001 2.00e-02 2.50e+03 pdb=" C4 U D 20 " 0.003 2.00e-02 2.50e+03 pdb=" O4 U D 20 " 0.006 2.00e-02 2.50e+03 pdb=" C5 U D 20 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U D 20 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 38 " 0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO A 39 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 39 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 39 " 0.021 5.00e-02 4.00e+02 ... (remaining 1300 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 394 2.69 - 3.24: 8735 3.24 - 3.79: 16669 3.79 - 4.35: 20645 4.35 - 4.90: 31638 Nonbonded interactions: 78081 Sorted by model distance: nonbonded pdb=" OD1 ASP A 733 " pdb=" ND2 ASN A 737 " model vdw 2.136 3.120 nonbonded pdb=" OG1 THR A 38 " pdb=" OD1 ASP A 40 " model vdw 2.198 3.040 nonbonded pdb=" O6 DG B 22 " pdb=" NZ LYS A 227 " model vdw 2.246 3.120 nonbonded pdb=" O2 U D 45 " pdb=" N4 C D 46 " model vdw 2.248 3.120 nonbonded pdb=" OD1 ASN A 737 " pdb=" NH2 ARG A 740 " model vdw 2.257 3.120 ... (remaining 78076 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.760 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 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 0.039 10653 Z= 0.279 Angle : 0.627 10.444 15177 Z= 0.444 Chirality : 0.037 0.166 1778 Planarity : 0.004 0.074 1303 Dihedral : 18.454 147.677 4546 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.30 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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: 0.54 (0.31), residues: 787 helix: 2.01 (0.30), residues: 297 sheet: 0.14 (0.46), residues: 134 loop : -1.01 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 889 TYR 0.016 0.001 TYR A 698 PHE 0.006 0.001 PHE A 917 TRP 0.021 0.002 TRP A 304 HIS 0.001 0.001 HIS A 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.28 (10652) covalent geometry : angle 0.62745 / 0.44 (15175) SS BOND : bond 0.00116 / 0.06 ( 1) SS BOND : angle 0.54146 / 0.77 ( 2) hydrogen bonds : bond 0.14720 / 16.52 ( 434) hydrogen bonds : angle 5.92054 / 7.83 ( 1115) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.207 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0820 time to fit residues: 7.7514 Evaluate side-chains 42 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.0970 chunk 74 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 ASN A 512 GLN A 804 GLN A 812 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.174258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.124640 restraints weight = 22045.525| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 3.13 r_work: 0.3628 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.0662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10653 Z= 0.131 Angle : 0.562 7.046 15177 Z= 0.313 Chirality : 0.036 0.143 1778 Planarity : 0.004 0.040 1303 Dihedral : 19.622 149.189 2892 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.43 % Favored : 96.44 % Rotamer: Outliers : 0.86 % Allowed : 5.29 % Favored : 93.86 % 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: 0.82 (0.31), residues: 787 helix: 2.18 (0.30), residues: 304 sheet: 0.50 (0.48), residues: 123 loop : -0.91 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 337 TYR 0.013 0.001 TYR A 244 PHE 0.008 0.001 PHE A 588 TRP 0.011 0.001 TRP A 304 HIS 0.002 0.001 HIS A 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.13 (10652) covalent geometry : angle 0.56218 / 0.31 (15175) SS BOND : bond 0.00042 / 0.02 ( 1) SS BOND : angle 0.70818 / 0.92 ( 2) hydrogen bonds : bond 0.05078 / 5.40 ( 434) hydrogen bonds : angle 4.82661 / 6.41 ( 1115) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.262 Fit side-chains REVERT: A 627 ARG cc_start: 0.8025 (mtt90) cc_final: 0.6795 (mtt180) outliers start: 6 outliers final: 1 residues processed: 53 average time/residue: 0.1012 time to fit residues: 7.5646 Evaluate side-chains 38 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 698 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 45 optimal weight: 3.9990 chunk 9 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 12 optimal weight: 30.0000 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 ASN A 924 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.171131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.120707 restraints weight = 22075.492| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 3.08 r_work: 0.3546 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10653 Z= 0.175 Angle : 0.591 7.671 15177 Z= 0.326 Chirality : 0.038 0.169 1778 Planarity : 0.005 0.046 1303 Dihedral : 19.633 144.102 2892 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.07 % Favored : 95.81 % Rotamer: Outliers : 1.29 % Allowed : 8.29 % Favored : 90.43 % 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: 0.50 (0.30), residues: 787 helix: 2.16 (0.30), residues: 298 sheet: -0.25 (0.46), residues: 132 loop : -1.04 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 337 TYR 0.022 0.002 TYR A 244 PHE 0.014 0.002 PHE A 588 TRP 0.013 0.002 TRP A 86 HIS 0.004 0.001 HIS A 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (10652) covalent geometry : angle 0.59105 / 0.33 (15175) SS BOND : bond 0.00234 / 0.12 ( 1) SS BOND : angle 0.44079 / 0.43 ( 2) hydrogen bonds : bond 0.05830 / 6.35 ( 434) hydrogen bonds : angle 4.42672 / 5.77 ( 1115) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.272 Fit side-chains REVERT: A 141 LYS cc_start: 0.6802 (ttmt) cc_final: 0.6430 (ttpp) REVERT: A 153 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.7977 (t) REVERT: A 618 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7929 (tm-30) REVERT: A 627 ARG cc_start: 0.8103 (mtt90) cc_final: 0.7586 (mtt-85) REVERT: A 660 ARG cc_start: 0.6310 (mtm180) cc_final: 0.4308 (ttp-110) REVERT: A 709 LYS cc_start: 0.7617 (ttmt) cc_final: 0.7183 (tttt) REVERT: A 775 GLN cc_start: 0.7893 (mp10) cc_final: 0.7675 (mp10) outliers start: 9 outliers final: 3 residues processed: 59 average time/residue: 0.1043 time to fit residues: 8.4500 Evaluate side-chains 48 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 698 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 35 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 65 optimal weight: 0.0270 chunk 21 optimal weight: 0.3980 chunk 79 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 54 optimal weight: 0.0770 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 812 ASN A 924 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.173683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.122879 restraints weight = 22345.449| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 3.18 r_work: 0.3620 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10653 Z= 0.116 Angle : 0.528 8.167 15177 Z= 0.296 Chirality : 0.035 0.142 1778 Planarity : 0.004 0.047 1303 Dihedral : 19.594 145.916 2892 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.43 % Favored : 96.44 % Rotamer: Outliers : 1.43 % Allowed : 9.57 % Favored : 89.00 % 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: 0.73 (0.31), residues: 787 helix: 2.23 (0.30), residues: 304 sheet: 0.11 (0.48), residues: 124 loop : -0.94 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 703 TYR 0.025 0.002 TYR A 622 PHE 0.008 0.001 PHE A 917 TRP 0.012 0.001 TRP A 304 HIS 0.002 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.12 (10652) covalent geometry : angle 0.52796 / 0.30 (15175) SS BOND : bond 0.00124 / 0.06 ( 1) SS BOND : angle 0.27579 / 0.30 ( 2) hydrogen bonds : bond 0.04765 / 5.02 ( 434) hydrogen bonds : angle 4.19957 / 5.47 ( 1115) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.274 Fit side-chains REVERT: A 141 LYS cc_start: 0.6748 (ttmt) cc_final: 0.6408 (ttpp) REVERT: A 618 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7823 (tm-30) REVERT: A 627 ARG cc_start: 0.7959 (mtt90) cc_final: 0.7554 (mtt-85) REVERT: A 709 LYS cc_start: 0.7622 (ttmt) cc_final: 0.7185 (tttm) outliers start: 10 outliers final: 4 residues processed: 59 average time/residue: 0.0972 time to fit residues: 8.1217 Evaluate side-chains 49 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 698 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 58 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 85 optimal weight: 0.0570 chunk 74 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 924 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.170788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.122639 restraints weight = 21965.284| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.85 r_work: 0.3563 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10653 Z= 0.171 Angle : 0.569 7.253 15177 Z= 0.315 Chirality : 0.037 0.157 1778 Planarity : 0.004 0.048 1303 Dihedral : 19.611 142.546 2892 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.57 % Favored : 95.30 % Rotamer: Outliers : 1.43 % Allowed : 11.86 % Favored : 86.71 % 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: 0.54 (0.31), residues: 787 helix: 2.27 (0.30), residues: 298 sheet: -0.32 (0.46), residues: 132 loop : -1.06 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 337 TYR 0.021 0.002 TYR A 244 PHE 0.015 0.002 PHE A 588 TRP 0.012 0.002 TRP A 304 HIS 0.003 0.001 HIS A 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (10652) covalent geometry : angle 0.56896 / 0.31 (15175) SS BOND : bond 0.00166 / 0.08 ( 1) SS BOND : angle 0.27132 / 0.17 ( 2) hydrogen bonds : bond 0.05593 / 6.09 ( 434) hydrogen bonds : angle 4.21085 / 5.45 ( 1115) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.223 Fit side-chains REVERT: A 141 LYS cc_start: 0.6859 (ttmt) cc_final: 0.6523 (ttpt) REVERT: A 153 THR cc_start: 0.8280 (OUTLIER) cc_final: 0.7868 (t) REVERT: A 247 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7555 (tp) REVERT: A 627 ARG cc_start: 0.7942 (mtt90) cc_final: 0.7485 (mtt-85) REVERT: A 660 ARG cc_start: 0.6279 (mtm180) cc_final: 0.4723 (ttp-110) REVERT: A 709 LYS cc_start: 0.7652 (ttmt) cc_final: 0.7230 (tttm) outliers start: 10 outliers final: 5 residues processed: 58 average time/residue: 0.0946 time to fit residues: 7.5839 Evaluate side-chains 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 698 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 60 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 88 optimal weight: 0.0070 chunk 40 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 63 optimal weight: 0.0070 chunk 69 optimal weight: 0.9990 chunk 47 optimal weight: 0.2980 chunk 14 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 284 GLN A 812 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.173288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.125670 restraints weight = 22230.235| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.95 r_work: 0.3622 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10653 Z= 0.115 Angle : 0.531 8.531 15177 Z= 0.297 Chirality : 0.035 0.144 1778 Planarity : 0.004 0.046 1303 Dihedral : 19.601 145.000 2892 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 1.00 % Allowed : 11.86 % Favored : 87.14 % 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: 0.73 (0.31), residues: 787 helix: 2.29 (0.30), residues: 304 sheet: 0.08 (0.48), residues: 125 loop : -0.99 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 627 TYR 0.014 0.001 TYR A 244 PHE 0.007 0.001 PHE A 332 TRP 0.014 0.001 TRP A 304 HIS 0.002 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.11 (10652) covalent geometry : angle 0.53058 / 0.30 (15175) SS BOND : bond 0.00126 / 0.06 ( 1) SS BOND : angle 0.19236 / 0.32 ( 2) hydrogen bonds : bond 0.04611 / 4.84 ( 434) hydrogen bonds : angle 4.01328 / 5.16 ( 1115) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.279 Fit side-chains REVERT: A 141 LYS cc_start: 0.6797 (ttmt) cc_final: 0.6407 (ttpp) REVERT: A 153 THR cc_start: 0.8262 (OUTLIER) cc_final: 0.7937 (t) REVERT: A 627 ARG cc_start: 0.7916 (mtt90) cc_final: 0.7547 (mtt-85) REVERT: A 660 ARG cc_start: 0.6144 (mtm180) cc_final: 0.4584 (ttp-110) REVERT: A 709 LYS cc_start: 0.7667 (ttmt) cc_final: 0.7273 (tttm) outliers start: 7 outliers final: 5 residues processed: 54 average time/residue: 0.1214 time to fit residues: 8.9028 Evaluate side-chains 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 698 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 40 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 92 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 945 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.166661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.111003 restraints weight = 21796.827| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 3.04 r_work: 0.3487 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 10653 Z= 0.314 Angle : 0.747 9.703 15177 Z= 0.403 Chirality : 0.045 0.198 1778 Planarity : 0.006 0.052 1303 Dihedral : 19.799 135.606 2892 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.59 % Favored : 94.28 % Rotamer: Outliers : 1.57 % Allowed : 12.43 % Favored : 86.00 % 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: -0.15 (0.30), residues: 787 helix: 1.68 (0.30), residues: 298 sheet: -0.68 (0.45), residues: 135 loop : -1.44 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 591 TYR 0.030 0.003 TYR A 244 PHE 0.030 0.003 PHE A 588 TRP 0.019 0.003 TRP A 86 HIS 0.006 0.002 HIS A 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00686 / 0.31 (10652) covalent geometry : angle 0.74731 / 0.40 (15175) SS BOND : bond 0.00110 / 0.05 ( 1) SS BOND : angle 0.69144 / 0.94 ( 2) hydrogen bonds : bond 0.07720 / 8.52 ( 434) hydrogen bonds : angle 4.57932 / 5.86 ( 1115) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.175 Fit side-chains REVERT: A 38 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8281 (p) REVERT: A 141 LYS cc_start: 0.6880 (ttmt) cc_final: 0.6548 (ttpt) REVERT: A 153 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8148 (t) REVERT: A 247 ILE cc_start: 0.7866 (OUTLIER) cc_final: 0.7486 (tp) REVERT: A 618 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7871 (tm-30) REVERT: A 627 ARG cc_start: 0.8006 (mtt90) cc_final: 0.7610 (mtt-85) REVERT: A 660 ARG cc_start: 0.6530 (mtm180) cc_final: 0.4641 (ttm110) REVERT: A 709 LYS cc_start: 0.7736 (ttmt) cc_final: 0.7417 (tttt) outliers start: 11 outliers final: 4 residues processed: 60 average time/residue: 0.1059 time to fit residues: 8.6747 Evaluate side-chains 54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 698 TYR Chi-restraints excluded: chain A residue 813 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 71 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 8 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.168547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.117920 restraints weight = 21891.503| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 3.24 r_work: 0.3491 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10653 Z= 0.192 Angle : 0.609 8.153 15177 Z= 0.335 Chirality : 0.039 0.166 1778 Planarity : 0.004 0.047 1303 Dihedral : 19.770 135.344 2892 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.96 % Favored : 94.92 % Rotamer: Outliers : 1.43 % Allowed : 14.14 % Favored : 84.43 % 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: -0.01 (0.30), residues: 787 helix: 1.86 (0.30), residues: 298 sheet: -0.73 (0.45), residues: 130 loop : -1.36 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 337 TYR 0.023 0.002 TYR A 244 PHE 0.015 0.002 PHE A 588 TRP 0.015 0.002 TRP A 304 HIS 0.005 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.19 (10652) covalent geometry : angle 0.60901 / 0.34 (15175) SS BOND : bond 0.00227 / 0.11 ( 1) SS BOND : angle 0.23100 / 0.15 ( 2) hydrogen bonds : bond 0.05941 / 6.43 ( 434) hydrogen bonds : angle 4.31428 / 5.54 ( 1115) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.280 Fit side-chains REVERT: A 38 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8069 (p) REVERT: A 141 LYS cc_start: 0.6881 (ttmt) cc_final: 0.6557 (ttpt) REVERT: A 153 THR cc_start: 0.8496 (OUTLIER) cc_final: 0.8118 (t) REVERT: A 247 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7582 (tp) REVERT: A 618 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7857 (tm-30) REVERT: A 627 ARG cc_start: 0.8069 (mtt90) cc_final: 0.7702 (mtt-85) REVERT: A 660 ARG cc_start: 0.6493 (mtm180) cc_final: 0.4836 (ttm110) REVERT: A 709 LYS cc_start: 0.7855 (ttmt) cc_final: 0.7621 (tttt) outliers start: 10 outliers final: 5 residues processed: 56 average time/residue: 0.1157 time to fit residues: 8.7745 Evaluate side-chains 55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 698 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 53 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.165981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.111023 restraints weight = 21746.669| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.97 r_work: 0.3484 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 10653 Z= 0.287 Angle : 0.711 8.489 15177 Z= 0.384 Chirality : 0.043 0.188 1778 Planarity : 0.005 0.051 1303 Dihedral : 19.891 134.094 2892 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.84 % Favored : 94.03 % Rotamer: Outliers : 1.86 % Allowed : 14.29 % Favored : 83.86 % 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: -0.39 (0.30), residues: 787 helix: 1.54 (0.30), residues: 298 sheet: -0.90 (0.45), residues: 130 loop : -1.59 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 42 TYR 0.027 0.003 TYR A 244 PHE 0.022 0.002 PHE A 588 TRP 0.017 0.003 TRP A 86 HIS 0.006 0.002 HIS A 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.29 (10652) covalent geometry : angle 0.71077 / 0.38 (15175) SS BOND : bond 0.00236 / 0.12 ( 1) SS BOND : angle 0.53055 / 0.42 ( 2) hydrogen bonds : bond 0.07152 / 7.84 ( 434) hydrogen bonds : angle 4.55872 / 5.85 ( 1115) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.277 Fit side-chains REVERT: A 38 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8226 (p) REVERT: A 141 LYS cc_start: 0.6907 (ttmt) cc_final: 0.6604 (ttpt) REVERT: A 153 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.8178 (t) REVERT: A 247 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7572 (tp) REVERT: A 618 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7884 (tm-30) REVERT: A 627 ARG cc_start: 0.8042 (mtt90) cc_final: 0.7655 (mtt-85) REVERT: A 660 ARG cc_start: 0.6522 (mtm180) cc_final: 0.4734 (ttm110) REVERT: A 709 LYS cc_start: 0.7967 (ttmt) cc_final: 0.7753 (tttt) outliers start: 13 outliers final: 5 residues processed: 58 average time/residue: 0.1202 time to fit residues: 9.4861 Evaluate side-chains 53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 698 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 72 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 84 optimal weight: 0.7980 chunk 34 optimal weight: 0.3980 chunk 77 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.169878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.122680 restraints weight = 21635.316| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 3.06 r_work: 0.3540 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10653 Z= 0.128 Angle : 0.581 7.983 15177 Z= 0.319 Chirality : 0.037 0.154 1778 Planarity : 0.004 0.046 1303 Dihedral : 19.841 136.284 2892 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.07 % Favored : 95.81 % Rotamer: Outliers : 1.00 % Allowed : 15.14 % Favored : 83.86 % 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: 0.17 (0.31), residues: 787 helix: 2.01 (0.30), residues: 298 sheet: -0.70 (0.45), residues: 128 loop : -1.23 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 337 TYR 0.018 0.001 TYR A 244 PHE 0.010 0.001 PHE A 332 TRP 0.030 0.002 TRP A 310 HIS 0.003 0.001 HIS A 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.13 (10652) covalent geometry : angle 0.58114 / 0.32 (15175) SS BOND : bond 0.00149 / 0.07 ( 1) SS BOND : angle 0.17697 / 0.26 ( 2) hydrogen bonds : bond 0.05142 / 5.50 ( 434) hydrogen bonds : angle 4.16793 / 5.34 ( 1115) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.280 Fit side-chains REVERT: A 141 LYS cc_start: 0.6852 (ttmt) cc_final: 0.6567 (ttpt) REVERT: A 153 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8145 (t) REVERT: A 618 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7876 (tm-30) REVERT: A 627 ARG cc_start: 0.7887 (mtt90) cc_final: 0.7559 (mtt-85) REVERT: A 660 ARG cc_start: 0.6396 (mtm180) cc_final: 0.4716 (ttm110) REVERT: A 709 LYS cc_start: 0.7907 (ttmt) cc_final: 0.7682 (tttt) outliers start: 7 outliers final: 5 residues processed: 52 average time/residue: 0.1217 time to fit residues: 8.4716 Evaluate side-chains 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 698 TYR Chi-restraints excluded: chain A residue 757 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 43 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 32 optimal weight: 0.0170 chunk 47 optimal weight: 0.7980 chunk 12 optimal weight: 30.0000 chunk 17 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 overall best weight: 1.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.169915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.115842 restraints weight = 21647.792| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.99 r_work: 0.3561 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.189 10653 Z= 0.211 Angle : 0.884 59.103 15177 Z= 0.522 Chirality : 0.037 0.201 1778 Planarity : 0.004 0.046 1303 Dihedral : 19.844 136.236 2892 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.19 % Favored : 95.68 % Rotamer: Outliers : 0.86 % Allowed : 15.14 % Favored : 84.00 % Cbeta Deviations : 0.13 % 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: 0.18 (0.31), residues: 787 helix: 2.01 (0.30), residues: 298 sheet: -0.69 (0.46), residues: 128 loop : -1.23 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 337 TYR 0.018 0.001 TYR A 244 PHE 0.010 0.001 PHE A 332 TRP 0.025 0.002 TRP A 310 HIS 0.003 0.001 HIS A 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.21 (10652) covalent geometry : angle 0.88378 / 0.52 (15175) SS BOND : bond 0.00154 / 0.08 ( 1) SS BOND : angle 0.15595 / 0.26 ( 2) hydrogen bonds : bond 0.05178 / 5.55 ( 434) hydrogen bonds : angle 4.16593 / 5.34 ( 1115) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2760.23 seconds wall clock time: 47 minutes 48.69 seconds (2868.69 seconds total)