Starting phenix.real_space_refine on Fri Sep 11 16:04:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wb0_32391/09_2026/7wb0_32391.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wb0_32391/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7wb0_32391/09_2026/7wb0_32391.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wb0_32391/09_2026/7wb0_32391.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wb0_32391/09_2026/7wb0_32391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wb0_32391/09_2026/7wb0_32391.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wb0_32391/09_2026/7wb0_32391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wb0_32391/09_2026/7wb0_32391.map" } 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-2.2.1-6174/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: {'RNAv2': 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: 2.18, per 1000 atoms: 0.22 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: 1.20 Conformation dependent library (CDL) restraints added in 254.1 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: 1.21 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: 2.41 Time building geometry restraints manager: 1.55 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: 14599 2.09 - 4.18: 535 4.18 - 6.27: 38 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 - 17.05: 4822 17.05 - 34.10: 725 34.10 - 51.15: 303 51.15 - 68.20: 174 68.20 - 85.25: 29 Dihedral angle restraints: 6053 sinusoidal: 3727 harmonic: 2326 Sorted by residual: dihedral pdb=" C4' C D 32 " pdb=" C3' C D 32 " pdb=" C2' C D 32 " pdb=" C1' C D 32 " ideal model delta sinusoidal sigma weight residual 36.34 -37.71 74.06 1 3.10e+00 1.04e-01 7.25e+02 dihedral pdb=" C4' A D 42 " pdb=" C3' A D 42 " pdb=" C2' A D 42 " pdb=" C1' A D 42 " ideal model delta sinusoidal sigma weight residual 36.34 -36.46 72.81 1 3.10e+00 1.04e-01 7.04e+02 dihedral pdb=" C4' C D 14 " pdb=" C3' C D 14 " pdb=" C2' C D 14 " pdb=" C1' C D 14 " ideal model delta sinusoidal sigma weight residual 36.34 -36.01 72.36 1 3.10e+00 1.04e-01 6.96e+02 ... (remaining 6050 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1431 0.059 - 0.117: 197 0.117 - 0.176: 9 0.176 - 0.235: 79 0.235 - 0.294: 62 Chirality restraints: 1778 Sorted by residual: chirality pdb=" C3' C D 32 " pdb=" C4' C D 32 " pdb=" O3' C D 32 " pdb=" C2' C D 32 " both_signs ideal model delta sigma weight residual False -2.50 -2.79 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C2' U D 43 " pdb=" C3' U D 43 " pdb=" O2' U D 43 " pdb=" C1' U D 43 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C2' U D 45 " pdb=" C3' U D 45 " pdb=" O2' U D 45 " pdb=" C1' U D 45 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.89e+00 ... (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: 1.380 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.120 Find NCS groups from input model: 0.030 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.010 ------------------------------------------------------------------------------- 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 : 0.004 0.039 10653 Z= 0.284 Angle : 0.763 10.444 15177 Z= 0.466 Chirality : 0.076 0.294 1778 Planarity : 0.004 0.074 1303 Dihedral : 20.177 85.248 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 0.00365 / 0.28 (10652) covalent geometry : angle 0.76279 / 0.47 (15175) SS BOND : bond 0.00116 / 0.06 ( 1) SS BOND : angle 0.54146 / 0.77 ( 2) hydrogen bonds : bond 0.14720 / 16.58 ( 434) hydrogen bonds : angle 5.92054 / 7.84 ( 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 : 0.287 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0935 time to fit residues: 8.8944 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 : 0.299 ------------------------------------------------------------------------------- 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: 6.9990 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 = 0.4574 r_free = 0.4574 target = 0.175003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.131153 restraints weight = 22267.844| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 3.29 r_work: 0.3621 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10653 Z= 0.180 Angle : 1.106 22.894 15177 Z= 0.466 Chirality : 0.112 1.481 1778 Planarity : 0.004 0.040 1303 Dihedral : 20.620 135.796 2892 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.56 % Favored : 96.32 % Rotamer: Outliers : 0.86 % Allowed : 5.00 % Favored : 94.14 % 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: 0.83 (0.31), residues: 787 helix: 2.20 (0.30), residues: 304 sheet: 0.48 (0.48), residues: 123 loop : -0.90 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 615 TYR 0.014 0.001 TYR A 244 PHE 0.013 0.001 PHE A 588 TRP 0.011 0.002 TRP A 304 HIS 0.004 0.001 HIS A 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.18 (10652) covalent geometry : angle 1.10623 / 0.47 (15175) SS BOND : bond 0.00066 / 0.03 ( 1) SS BOND : angle 0.61143 / 0.85 ( 2) hydrogen bonds : bond 0.04933 / 5.29 ( 434) hydrogen bonds : angle 4.75234 / 6.31 ( 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 59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 627 ARG cc_start: 0.8078 (mtt90) cc_final: 0.6833 (mtt180) outliers start: 6 outliers final: 1 residues processed: 56 average time/residue: 0.1237 time to fit residues: 9.7699 Evaluate side-chains 42 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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: 20.0000 chunk 9 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 0.0060 chunk 0 optimal weight: 40.0000 overall best weight: 3.7402 ------------------------------------------------------------------------------- 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 = 0.4511 r_free = 0.4511 target = 0.169399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.119238 restraints weight = 21961.254| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 3.27 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10653 Z= 0.252 Angle : 0.946 12.714 15177 Z= 0.432 Chirality : 0.080 0.781 1778 Planarity : 0.005 0.048 1303 Dihedral : 20.485 158.376 2892 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.08 % Favored : 94.79 % Rotamer: Outliers : 1.43 % Allowed : 9.29 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.30), residues: 787 helix: 1.87 (0.30), residues: 298 sheet: -0.33 (0.46), residues: 135 loop : -1.20 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 12 TYR 0.027 0.003 TYR A 244 PHE 0.024 0.002 PHE A 588 TRP 0.016 0.002 TRP A 86 HIS 0.005 0.002 HIS A 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.25 (10652) covalent geometry : angle 0.94605 / 0.43 (15175) SS BOND : bond 0.00260 / 0.13 ( 1) SS BOND : angle 0.51026 / 0.35 ( 2) hydrogen bonds : bond 0.07014 / 7.69 ( 434) hydrogen bonds : angle 4.62270 / 6.06 ( 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 58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 153 THR cc_start: 0.8282 (OUTLIER) cc_final: 0.7879 (t) REVERT: A 247 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7260 (tp) REVERT: A 618 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7517 (tm-30) REVERT: A 627 ARG cc_start: 0.8032 (mtt90) cc_final: 0.7536 (mtt-85) REVERT: A 660 ARG cc_start: 0.5913 (mtm180) cc_final: 0.4281 (ttp-110) outliers start: 10 outliers final: 6 residues processed: 56 average time/residue: 0.1153 time to fit residues: 8.9979 Evaluate side-chains 48 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 645 LEU Chi-restraints excluded: chain A residue 698 TYR Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 779 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 35 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 54 optimal weight: 0.0470 chunk 45 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 13 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 overall best weight: 2.1884 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.170959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.122219 restraints weight = 22430.966| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 3.07 r_work: 0.3539 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10653 Z= 0.178 Angle : 0.845 12.485 15177 Z= 0.382 Chirality : 0.069 0.629 1778 Planarity : 0.004 0.049 1303 Dihedral : 20.328 159.950 2892 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.70 % Favored : 95.17 % Rotamer: Outliers : 1.43 % Allowed : 11.29 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.31), residues: 787 helix: 2.10 (0.30), residues: 298 sheet: -0.42 (0.46), residues: 132 loop : -1.13 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 12 TYR 0.022 0.002 TYR A 244 PHE 0.013 0.001 PHE A 588 TRP 0.013 0.002 TRP A 598 HIS 0.004 0.001 HIS A 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.18 (10652) covalent geometry : angle 0.84456 / 0.38 (15175) SS BOND : bond 0.00192 / 0.10 ( 1) SS BOND : angle 0.39785 / 0.53 ( 2) hydrogen bonds : bond 0.05665 / 6.11 ( 434) hydrogen bonds : angle 4.35440 / 5.72 ( 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 58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 627 ARG cc_start: 0.8052 (mtt90) cc_final: 0.7647 (mtt-85) REVERT: A 660 ARG cc_start: 0.6407 (mtm180) cc_final: 0.4317 (ttm110) REVERT: A 709 LYS cc_start: 0.7546 (ttmt) cc_final: 0.7143 (tttt) outliers start: 10 outliers final: 5 residues processed: 54 average time/residue: 0.1091 time to fit residues: 8.0447 Evaluate side-chains 48 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 698 TYR Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 813 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 58 optimal weight: 0.9980 chunk 19 optimal weight: 0.0370 chunk 36 optimal weight: 0.8980 chunk 85 optimal weight: 20.0000 chunk 74 optimal weight: 0.0670 chunk 48 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.4570 r_free = 0.4570 target = 0.173992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.124241 restraints weight = 22564.406| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 3.10 r_work: 0.3622 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1920 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= 0.130 Angle : 0.769 11.814 15177 Z= 0.347 Chirality : 0.061 0.539 1778 Planarity : 0.004 0.047 1303 Dihedral : 20.243 177.078 2892 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.94 % Favored : 95.93 % Rotamer: Outliers : 1.71 % Allowed : 11.43 % Favored : 86.86 % 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: 0.69 (0.31), residues: 787 helix: 2.39 (0.30), residues: 298 sheet: -0.27 (0.47), residues: 132 loop : -0.96 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 337 TYR 0.014 0.001 TYR A 244 PHE 0.009 0.001 PHE A 509 TRP 0.013 0.001 TRP A 962 HIS 0.002 0.001 HIS A 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.13 (10652) covalent geometry : angle 0.76950 / 0.35 (15175) SS BOND : bond 0.00095 / 0.05 ( 1) SS BOND : angle 0.13724 / 0.27 ( 2) hydrogen bonds : bond 0.04845 / 5.15 ( 434) hydrogen bonds : angle 4.06680 / 5.33 ( 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 64 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 153 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.7826 (t) REVERT: A 627 ARG cc_start: 0.8009 (mtt90) cc_final: 0.7588 (mtt-85) REVERT: A 660 ARG cc_start: 0.6293 (mtm180) cc_final: 0.4556 (ttm110) REVERT: A 709 LYS cc_start: 0.7632 (ttmt) cc_final: 0.7247 (tttm) outliers start: 12 outliers final: 6 residues processed: 60 average time/residue: 0.1198 time to fit residues: 9.8399 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 : 0.283 ------------------------------------------------------------------------------- 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 570 MET Chi-restraints excluded: chain A residue 698 TYR Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 813 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 60 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 = 0.4503 r_free = 0.4503 target = 0.168385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.118047 restraints weight = 22462.277| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 3.05 r_work: 0.3487 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 10653 Z= 0.288 Angle : 0.912 11.159 15177 Z= 0.416 Chirality : 0.068 0.647 1778 Planarity : 0.005 0.054 1303 Dihedral : 20.291 170.226 2892 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.34 % Favored : 94.54 % Rotamer: Outliers : 2.43 % Allowed : 12.86 % Favored : 84.71 % 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: 0.13 (0.30), residues: 787 helix: 1.94 (0.30), residues: 298 sheet: -0.68 (0.46), residues: 132 loop : -1.25 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 12 TYR 0.028 0.002 TYR A 244 PHE 0.026 0.002 PHE A 588 TRP 0.015 0.003 TRP A 86 HIS 0.006 0.002 HIS A 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.29 (10652) covalent geometry : angle 0.91251 / 0.42 (15175) SS BOND : bond 0.00188 / 0.09 ( 1) SS BOND : angle 0.40477 / 0.29 ( 2) hydrogen bonds : bond 0.06824 / 7.45 ( 434) hydrogen bonds : angle 4.42316 / 5.76 ( 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 69 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 153 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.7964 (t) REVERT: A 247 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7450 (tp) REVERT: A 529 LEU cc_start: 0.8570 (mt) cc_final: 0.7880 (mt) REVERT: A 618 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7839 (tm-30) REVERT: A 660 ARG cc_start: 0.6518 (mtm180) cc_final: 0.4917 (ttm110) REVERT: A 709 LYS cc_start: 0.7682 (ttmt) cc_final: 0.7356 (tttt) REVERT: A 723 TYR cc_start: 0.5405 (m-80) cc_final: 0.4687 (m-80) outliers start: 17 outliers final: 8 residues processed: 65 average time/residue: 0.1163 time to fit residues: 10.3105 Evaluate side-chains 58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 645 LEU Chi-restraints excluded: chain A residue 698 TYR Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 962 TRP 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: 0.4980 chunk 86 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 92 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 = 0.4528 r_free = 0.4528 target = 0.170410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.121805 restraints weight = 22452.817| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.95 r_work: 0.3532 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10653 Z= 0.177 Angle : 0.820 11.446 15177 Z= 0.373 Chirality : 0.063 0.566 1778 Planarity : 0.004 0.049 1303 Dihedral : 20.277 170.502 2892 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.83 % Favored : 95.04 % Rotamer: Outliers : 1.71 % Allowed : 14.14 % Favored : 84.14 % 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: 0.25 (0.31), residues: 787 helix: 2.10 (0.30), residues: 298 sheet: -0.71 (0.46), residues: 132 loop : -1.19 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 337 TYR 0.021 0.002 TYR A 244 PHE 0.015 0.001 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 0.00365 / 0.18 (10652) covalent geometry : angle 0.82055 / 0.37 (15175) SS BOND : bond 0.00206 / 0.10 ( 1) SS BOND : angle 0.26352 / 0.18 ( 2) hydrogen bonds : bond 0.05745 / 6.22 ( 434) hydrogen bonds : angle 4.24356 / 5.53 ( 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 59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 153 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.7943 (t) REVERT: A 247 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7565 (tp) REVERT: A 618 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7812 (tm-30) REVERT: A 627 ARG cc_start: 0.7833 (mtt90) cc_final: 0.7559 (mtt-85) REVERT: A 660 ARG cc_start: 0.6473 (mtm180) cc_final: 0.4750 (ttm110) REVERT: A 709 LYS cc_start: 0.7797 (ttmt) cc_final: 0.7534 (tttt) REVERT: A 723 TYR cc_start: 0.5328 (m-80) cc_final: 0.4616 (m-80) outliers start: 12 outliers final: 9 residues processed: 57 average time/residue: 0.1279 time to fit residues: 9.8348 Evaluate side-chains 56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 220 CYS Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 298 VAL 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 Chi-restraints excluded: chain A residue 702 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 71 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.168381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.117359 restraints weight = 22100.912| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 3.02 r_work: 0.3492 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 10653 Z= 0.233 Angle : 0.878 11.010 15177 Z= 0.401 Chirality : 0.066 0.632 1778 Planarity : 0.005 0.052 1303 Dihedral : 20.348 172.003 2892 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.72 % Favored : 94.16 % Rotamer: Outliers : 2.14 % Allowed : 14.71 % Favored : 83.14 % 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: -0.02 (0.30), residues: 787 helix: 1.83 (0.30), residues: 298 sheet: -0.70 (0.47), residues: 128 loop : -1.37 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 49 TYR 0.023 0.002 TYR A 244 PHE 0.023 0.002 PHE A 588 TRP 0.016 0.002 TRP A 304 HIS 0.005 0.002 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.23 (10652) covalent geometry : angle 0.87769 / 0.40 (15175) SS BOND : bond 0.00224 / 0.11 ( 1) SS BOND : angle 0.40966 / 0.74 ( 2) hydrogen bonds : bond 0.06525 / 7.12 ( 434) hydrogen bonds : angle 4.39257 / 5.70 ( 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 63 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8098 (p) REVERT: A 153 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8131 (t) REVERT: A 247 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7640 (tp) REVERT: A 618 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7889 (tm-30) REVERT: A 627 ARG cc_start: 0.7840 (mtt90) cc_final: 0.7525 (mtt-85) REVERT: A 660 ARG cc_start: 0.6586 (mtm180) cc_final: 0.4981 (ttm110) REVERT: A 709 LYS cc_start: 0.7923 (ttmt) cc_final: 0.7704 (tttt) REVERT: A 723 TYR cc_start: 0.5572 (m-80) cc_final: 0.4865 (m-80) outliers start: 15 outliers final: 11 residues processed: 59 average time/residue: 0.1244 time to fit residues: 10.0892 Evaluate side-chains 58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 220 CYS Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 298 VAL 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 Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 813 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 53 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.169772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.120590 restraints weight = 22116.449| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 3.19 r_work: 0.3518 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10653 Z= 0.174 Angle : 0.820 10.987 15177 Z= 0.373 Chirality : 0.063 0.564 1778 Planarity : 0.004 0.049 1303 Dihedral : 20.334 170.395 2892 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.34 % Favored : 94.54 % Rotamer: Outliers : 2.00 % Allowed : 14.86 % Favored : 83.14 % 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: 0.12 (0.31), residues: 787 helix: 1.95 (0.30), residues: 298 sheet: -0.78 (0.46), residues: 130 loop : -1.22 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 49 TYR 0.020 0.001 TYR A 244 PHE 0.014 0.001 PHE A 588 TRP 0.016 0.002 TRP A 304 HIS 0.003 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (10652) covalent geometry : angle 0.82034 / 0.37 (15175) SS BOND : bond 0.00174 / 0.09 ( 1) SS BOND : angle 0.24896 / 0.17 ( 2) hydrogen bonds : bond 0.05708 / 6.16 ( 434) hydrogen bonds : angle 4.24609 / 5.52 ( 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 63 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8100 (t) REVERT: A 247 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7560 (tp) REVERT: A 618 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7882 (tm-30) REVERT: A 627 ARG cc_start: 0.7774 (mtt90) cc_final: 0.7482 (mtt-85) REVERT: A 660 ARG cc_start: 0.6475 (mtm180) cc_final: 0.4730 (ttm110) REVERT: A 723 TYR cc_start: 0.5643 (m-80) cc_final: 0.4950 (m-80) outliers start: 14 outliers final: 9 residues processed: 59 average time/residue: 0.1182 time to fit residues: 9.6754 Evaluate side-chains 58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 298 VAL Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 698 TYR Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 784 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.171013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.123016 restraints weight = 22234.686| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.89 r_work: 0.3559 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10653 Z= 0.153 Angle : 0.800 10.825 15177 Z= 0.364 Chirality : 0.061 0.532 1778 Planarity : 0.004 0.049 1303 Dihedral : 20.300 172.877 2892 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.70 % Favored : 95.17 % Rotamer: Outliers : 1.71 % Allowed : 15.43 % Favored : 82.86 % 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: 0.26 (0.31), residues: 787 helix: 2.05 (0.30), residues: 298 sheet: -0.69 (0.46), residues: 130 loop : -1.13 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 337 TYR 0.018 0.001 TYR A 244 PHE 0.012 0.001 PHE A 588 TRP 0.017 0.002 TRP A 304 HIS 0.003 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (10652) covalent geometry : angle 0.79996 / 0.36 (15175) SS BOND : bond 0.00114 / 0.06 ( 1) SS BOND : angle 0.29049 / 0.18 ( 2) hydrogen bonds : bond 0.05380 / 5.81 ( 434) hydrogen bonds : angle 4.16625 / 5.40 ( 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 59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 153 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8142 (t) REVERT: A 247 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7520 (tp) REVERT: A 618 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7829 (tm-30) REVERT: A 627 ARG cc_start: 0.7664 (mtt90) cc_final: 0.7383 (mtt-85) REVERT: A 660 ARG cc_start: 0.6496 (mtm180) cc_final: 0.4670 (ttm110) REVERT: A 702 GLN cc_start: 0.6951 (OUTLIER) cc_final: 0.6619 (tp40) outliers start: 12 outliers final: 8 residues processed: 56 average time/residue: 0.1271 time to fit residues: 9.6616 Evaluate side-chains 58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 298 VAL Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 698 TYR Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 784 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 43 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 chunk 17 optimal weight: 0.0870 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 812 ASN ** 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 = 0.4549 r_free = 0.4549 target = 0.172471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.124614 restraints weight = 22234.280| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 3.07 r_work: 0.3580 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10653 Z= 0.135 Angle : 0.779 10.646 15177 Z= 0.353 Chirality : 0.059 0.490 1778 Planarity : 0.004 0.048 1303 Dihedral : 20.231 173.621 2892 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.45 % Favored : 95.43 % Rotamer: Outliers : 1.14 % Allowed : 16.29 % Favored : 82.57 % 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: 0.42 (0.31), residues: 787 helix: 2.14 (0.30), residues: 298 sheet: -0.61 (0.46), residues: 132 loop : -0.99 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 49 TYR 0.015 0.001 TYR A 244 PHE 0.011 0.001 PHE A 332 TRP 0.016 0.002 TRP A 304 HIS 0.003 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (10652) covalent geometry : angle 0.77878 / 0.35 (15175) SS BOND : bond 0.00106 / 0.05 ( 1) SS BOND : angle 0.08694 / 0.13 ( 2) hydrogen bonds : bond 0.04914 / 5.24 ( 434) hydrogen bonds : angle 4.07650 / 5.26 ( 1115) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3013.54 seconds wall clock time: 52 minutes 7.91 seconds (3127.91 seconds total)