Starting phenix.real_space_refine on Sat Aug 23 06:16:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wb0_32391/08_2025/7wb0_32391.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wb0_32391/08_2025/7wb0_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 { model { file = "/net/cci-nas-00/data/ceres_data/7wb0_32391/08_2025/7wb0_32391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wb0_32391/08_2025/7wb0_32391.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wb0_32391/08_2025/7wb0_32391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wb0_32391/08_2025/7wb0_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.19, 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: 0.67 Conformation dependent library (CDL) restraints added in 184.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.89 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: 1.84 Time building geometry restraints manager: 0.89 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=" CA ASP A 522 " pdb=" CB ASP A 522 " ideal model delta sigma weight residual 1.522 1.539 -0.017 1.27e-02 6.20e+03 1.88e+00 bond pdb=" C ALA A 320 " pdb=" N LYS A 321 " ideal model delta sigma weight residual 1.331 1.357 -0.026 2.07e-02 2.33e+03 1.63e+00 bond pdb=" C LYS A 210 " pdb=" O LYS A 210 " ideal model delta sigma weight residual 1.249 1.239 0.010 8.50e-03 1.38e+04 1.45e+00 bond pdb=" CG GLN A 702 " pdb=" CD GLN A 702 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.43e+00 bond pdb=" CA ASN A 528 " pdb=" C ASN A 528 " ideal model delta sigma weight residual 1.522 1.534 -0.013 1.08e-02 8.57e+03 1.35e+00 ... (remaining 10647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 14949 2.09 - 4.18: 207 4.18 - 6.27: 16 6.27 - 8.35: 2 8.35 - 10.44: 1 Bond angle restraints: 15175 Sorted by residual: angle pdb=" C LYS A 899 " pdb=" N ARG A 900 " pdb=" CA ARG A 900 " ideal model delta sigma weight residual 121.54 127.66 -6.12 1.91e+00 2.74e-01 1.03e+01 angle pdb=" C LYS A 701 " pdb=" N GLN A 702 " pdb=" CA GLN A 702 " ideal model delta sigma weight residual 120.72 115.48 5.24 1.67e+00 3.59e-01 9.83e+00 angle pdb=" C LEU A 529 " pdb=" N TYR A 530 " pdb=" CA TYR A 530 " ideal model delta sigma weight residual 121.87 126.97 -5.10 1.64e+00 3.72e-01 9.67e+00 angle pdb=" C PHE A 901 " pdb=" N SER A 902 " pdb=" CA SER A 902 " ideal model delta sigma weight residual 122.56 117.92 4.64 1.50e+00 4.44e-01 9.58e+00 angle pdb=" N GLN A 702 " pdb=" CA GLN A 702 " pdb=" CB GLN A 702 " ideal model delta sigma weight residual 110.39 115.51 -5.12 1.66e+00 3.63e-01 9.53e+00 ... (remaining 15170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.54: 5699 29.54 - 59.07: 599 59.07 - 88.61: 128 88.61 - 118.14: 2 118.14 - 147.68: 1 Dihedral angle restraints: 6429 sinusoidal: 4103 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 6426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1355 0.033 - 0.067: 313 0.067 - 0.100: 72 0.100 - 0.133: 36 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: 1.490 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.080 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 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 0.030 10653 Z= 0.133 Angle : 0.579 10.444 15177 Z= 0.323 Chirality : 0.034 0.166 1778 Planarity : 0.004 0.074 1303 Dihedral : 21.369 147.677 4922 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 aren 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 covalent geometry : bond 0.00259 (10652) covalent geometry : angle 0.57858 (15175) SS BOND : bond 0.00116 ( 1) SS BOND : angle 0.54146 ( 2) hydrogen bonds : bond 0.14720 ( 434) hydrogen bonds : angle 5.92054 ( 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 : 0.212 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0799 time to fit residues: 7.5541 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 : 0.182 ------------------------------------------------------------------------------- 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: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 chunk 74 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 GLN A 804 GLN A 812 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.173714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.122834 restraints weight = 22145.575| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 3.11 r_work: 0.3614 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10653 Z= 0.125 Angle : 0.538 7.020 15177 Z= 0.288 Chirality : 0.034 0.138 1778 Planarity : 0.004 0.046 1303 Dihedral : 23.286 148.712 3268 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 0.43 % Allowed : 6.00 % Favored : 93.57 % 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 aren not related in a simple way. whole: 0.82 (0.31), residues: 787 helix: 2.23 (0.30), residues: 304 sheet: 0.35 (0.48), residues: 123 loop : -0.90 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 337 TYR 0.017 0.001 TYR A 244 PHE 0.009 0.001 PHE A 588 TRP 0.010 0.002 TRP A 304 HIS 0.002 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00260 (10652) covalent geometry : angle 0.53796 (15175) SS BOND : bond 0.00085 ( 1) SS BOND : angle 0.65530 ( 2) hydrogen bonds : bond 0.04851 ( 434) hydrogen bonds : angle 4.37954 ( 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 56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.242 Fit side-chains REVERT: A 141 LYS cc_start: 0.6810 (ttmt) cc_final: 0.6173 (ttpt) REVERT: A 618 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7822 (tm-30) REVERT: A 627 ARG cc_start: 0.8099 (mtt90) cc_final: 0.7637 (mtt-85) REVERT: A 709 LYS cc_start: 0.7513 (ttmt) cc_final: 0.7079 (tttm) REVERT: A 723 TYR cc_start: 0.5031 (m-80) cc_final: 0.4100 (m-80) outliers start: 3 outliers final: 1 residues processed: 55 average time/residue: 0.0974 time to fit residues: 7.5024 Evaluate side-chains 41 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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: 9.9990 chunk 9 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 12 optimal weight: 30.0000 chunk 68 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 924 GLN A 945 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.166327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.116627 restraints weight = 22024.102| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 3.15 r_work: 0.3462 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 10653 Z= 0.294 Angle : 0.731 8.695 15177 Z= 0.388 Chirality : 0.043 0.205 1778 Planarity : 0.006 0.054 1303 Dihedral : 23.540 128.939 3268 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.84 % Favored : 94.03 % Rotamer: Outliers : 1.57 % Allowed : 9.43 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.30), residues: 787 helix: 1.50 (0.30), residues: 297 sheet: -0.50 (0.44), residues: 133 loop : -1.37 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 615 TYR 0.031 0.003 TYR A 244 PHE 0.017 0.002 PHE A 556 TRP 0.019 0.003 TRP A 86 HIS 0.006 0.002 HIS A 920 Details of bonding type rmsd covalent geometry : bond 0.00659 (10652) covalent geometry : angle 0.73118 (15175) SS BOND : bond 0.00265 ( 1) SS BOND : angle 0.70422 ( 2) hydrogen bonds : bond 0.07550 ( 434) hydrogen bonds : angle 4.73679 ( 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 68 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 141 LYS cc_start: 0.6955 (ttmt) cc_final: 0.6635 (ttpt) REVERT: A 153 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.7969 (t) REVERT: A 247 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7640 (tp) REVERT: A 306 ASN cc_start: 0.6750 (t0) cc_final: 0.6366 (t0) REVERT: A 618 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8071 (tm-30) REVERT: A 627 ARG cc_start: 0.8262 (mtt90) cc_final: 0.7846 (mtt-85) REVERT: A 660 ARG cc_start: 0.6579 (mtm180) cc_final: 0.4758 (ttm110) REVERT: A 709 LYS cc_start: 0.7899 (ttmt) cc_final: 0.7698 (tttt) outliers start: 11 outliers final: 5 residues processed: 66 average time/residue: 0.0989 time to fit residues: 9.0557 Evaluate side-chains 53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 698 TYR Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 962 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 35 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 65 optimal weight: 0.4980 chunk 21 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 ASN 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 = 0.169248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.117100 restraints weight = 22208.109| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 3.07 r_work: 0.3536 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10653 Z= 0.148 Angle : 0.566 8.227 15177 Z= 0.306 Chirality : 0.036 0.135 1778 Planarity : 0.004 0.052 1303 Dihedral : 23.308 133.665 3268 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.07 % Favored : 95.81 % Rotamer: Outliers : 0.86 % Allowed : 13.00 % Favored : 86.14 % 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 aren not related in a simple way. whole: 0.26 (0.31), residues: 787 helix: 1.99 (0.30), residues: 298 sheet: -0.39 (0.45), residues: 133 loop : -1.22 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 615 TYR 0.020 0.001 TYR A 244 PHE 0.010 0.001 PHE A 588 TRP 0.012 0.002 TRP A 598 HIS 0.003 0.001 HIS A 903 Details of bonding type rmsd covalent geometry : bond 0.00316 (10652) covalent geometry : angle 0.56599 (15175) SS BOND : bond 0.00071 ( 1) SS BOND : angle 0.17593 ( 2) hydrogen bonds : bond 0.05404 ( 434) hydrogen bonds : angle 4.18912 ( 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 57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 LYS cc_start: 0.6935 (ttmt) cc_final: 0.6542 (ttpp) REVERT: A 627 ARG cc_start: 0.8201 (mtt90) cc_final: 0.7727 (mtt-85) REVERT: A 660 ARG cc_start: 0.6554 (mtm180) cc_final: 0.4981 (ttm110) outliers start: 6 outliers final: 4 residues processed: 54 average time/residue: 0.1247 time to fit residues: 8.8072 Evaluate side-chains 51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 58 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.164916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.115072 restraints weight = 21558.260| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 3.11 r_work: 0.3444 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10653 Z= 0.246 Angle : 0.658 8.585 15177 Z= 0.352 Chirality : 0.039 0.155 1778 Planarity : 0.005 0.053 1303 Dihedral : 23.468 132.257 3268 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.10 % Favored : 93.77 % Rotamer: Outliers : 2.14 % Allowed : 14.43 % Favored : 83.43 % 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 aren not related in a simple way. whole: -0.03 (0.30), residues: 787 helix: 1.72 (0.30), residues: 298 sheet: -0.57 (0.46), residues: 133 loop : -1.34 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 615 TYR 0.027 0.002 TYR A 244 PHE 0.014 0.002 PHE A 551 TRP 0.017 0.002 TRP A 86 HIS 0.004 0.001 HIS A 920 Details of bonding type rmsd covalent geometry : bond 0.00549 (10652) covalent geometry : angle 0.65849 (15175) SS BOND : bond 0.00205 ( 1) SS BOND : angle 0.38269 ( 2) hydrogen bonds : bond 0.06642 ( 434) hydrogen bonds : angle 4.46599 ( 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 71 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 141 LYS cc_start: 0.6849 (ttmt) cc_final: 0.6557 (ttpt) REVERT: A 153 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.8175 (t) REVERT: A 247 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7569 (tp) REVERT: A 306 ASN cc_start: 0.6759 (t0) cc_final: 0.5587 (t0) REVERT: A 618 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7796 (tm-30) REVERT: A 624 ARG cc_start: 0.7539 (ptp90) cc_final: 0.7217 (mtm-85) REVERT: A 627 ARG cc_start: 0.8240 (mtt90) cc_final: 0.7715 (mtt-85) REVERT: A 660 ARG cc_start: 0.6589 (mtm180) cc_final: 0.4586 (ttm110) REVERT: A 754 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8199 (mt) REVERT: A 776 TYR cc_start: 0.5674 (OUTLIER) cc_final: 0.3509 (m-80) outliers start: 15 outliers final: 5 residues processed: 67 average time/residue: 0.1152 time to fit residues: 10.4044 Evaluate side-chains 56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 503 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 754 ILE Chi-restraints excluded: chain A residue 776 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 60 optimal weight: 0.0060 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 88 optimal weight: 0.0170 chunk 40 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 69 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.5834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.172026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.125421 restraints weight = 22459.393| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 3.08 r_work: 0.3591 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10653 Z= 0.114 Angle : 0.533 9.173 15177 Z= 0.287 Chirality : 0.034 0.130 1778 Planarity : 0.004 0.049 1303 Dihedral : 23.242 138.615 3268 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.18 % Favored : 96.70 % Rotamer: Outliers : 1.29 % Allowed : 15.86 % 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 aren not related in a simple way. whole: 0.51 (0.31), residues: 787 helix: 2.24 (0.30), residues: 298 sheet: -0.27 (0.46), residues: 128 loop : -1.10 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 337 TYR 0.014 0.001 TYR A 622 PHE 0.010 0.001 PHE A 509 TRP 0.017 0.001 TRP A 962 HIS 0.002 0.001 HIS A 903 Details of bonding type rmsd covalent geometry : bond 0.00236 (10652) covalent geometry : angle 0.53311 (15175) SS BOND : bond 0.00053 ( 1) SS BOND : angle 0.13339 ( 2) hydrogen bonds : bond 0.04557 ( 434) hydrogen bonds : angle 3.95959 ( 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 65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.295 Fit side-chains REVERT: A 141 LYS cc_start: 0.6952 (ttmt) cc_final: 0.6679 (ttpt) REVERT: A 618 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7740 (tm-30) REVERT: A 627 ARG cc_start: 0.7856 (mtt90) cc_final: 0.7411 (mtt-85) REVERT: A 660 ARG cc_start: 0.6446 (mtm180) cc_final: 0.4832 (ttm110) REVERT: A 702 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.6949 (tp-100) REVERT: A 754 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8353 (mp) REVERT: A 776 TYR cc_start: 0.5379 (OUTLIER) cc_final: 0.3531 (m-80) outliers start: 9 outliers final: 3 residues processed: 61 average time/residue: 0.1315 time to fit residues: 10.7284 Evaluate side-chains 53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 698 TYR Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 813 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 40 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 81 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 GLN ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.171112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.123343 restraints weight = 22205.330| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 3.16 r_work: 0.3540 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10653 Z= 0.126 Angle : 0.531 9.030 15177 Z= 0.287 Chirality : 0.034 0.131 1778 Planarity : 0.004 0.048 1303 Dihedral : 23.230 139.027 3268 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.19 % Favored : 95.68 % Rotamer: Outliers : 1.43 % Allowed : 16.57 % Favored : 82.00 % 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 aren not related in a simple way. whole: 0.51 (0.31), residues: 787 helix: 2.18 (0.30), residues: 304 sheet: -0.46 (0.46), residues: 135 loop : -1.01 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 337 TYR 0.015 0.001 TYR A 244 PHE 0.018 0.001 PHE A 815 TRP 0.014 0.001 TRP A 304 HIS 0.002 0.001 HIS A 920 Details of bonding type rmsd covalent geometry : bond 0.00269 (10652) covalent geometry : angle 0.53141 (15175) SS BOND : bond 0.00084 ( 1) SS BOND : angle 0.24790 ( 2) hydrogen bonds : bond 0.04707 ( 434) hydrogen bonds : angle 3.95388 ( 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 57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.261 Fit side-chains REVERT: A 141 LYS cc_start: 0.6955 (ttmt) cc_final: 0.6599 (ttpt) REVERT: A 153 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8364 (t) REVERT: A 618 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7807 (tm-30) REVERT: A 627 ARG cc_start: 0.7795 (mtt90) cc_final: 0.7348 (mtt-85) REVERT: A 660 ARG cc_start: 0.6533 (mtm180) cc_final: 0.4803 (ttm110) REVERT: A 702 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6974 (tp-100) REVERT: A 754 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8170 (mp) REVERT: A 776 TYR cc_start: 0.5602 (OUTLIER) cc_final: 0.3609 (m-80) REVERT: A 954 ASP cc_start: 0.1065 (OUTLIER) cc_final: 0.0831 (t0) outliers start: 10 outliers final: 3 residues processed: 54 average time/residue: 0.1214 time to fit residues: 8.8724 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 : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR 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 754 ILE Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 954 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 71 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4511 r_free = 0.4511 target = 0.169178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.122892 restraints weight = 21952.699| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 3.29 r_work: 0.3505 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10653 Z= 0.156 Angle : 0.561 9.810 15177 Z= 0.302 Chirality : 0.035 0.134 1778 Planarity : 0.004 0.047 1303 Dihedral : 23.240 137.010 3268 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.32 % Favored : 95.55 % Rotamer: Outliers : 1.57 % Allowed : 16.71 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.31), residues: 787 helix: 2.22 (0.30), residues: 298 sheet: -0.61 (0.45), residues: 135 loop : -1.07 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 337 TYR 0.020 0.001 TYR A 244 PHE 0.013 0.001 PHE A 588 TRP 0.016 0.002 TRP A 304 HIS 0.003 0.001 HIS A 920 Details of bonding type rmsd covalent geometry : bond 0.00340 (10652) covalent geometry : angle 0.56121 (15175) SS BOND : bond 0.00108 ( 1) SS BOND : angle 0.21467 ( 2) hydrogen bonds : bond 0.05251 ( 434) hydrogen bonds : angle 4.05320 ( 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: 11 poor density : 49 time to evaluate : 0.290 Fit side-chains REVERT: A 141 LYS cc_start: 0.6862 (ttmt) cc_final: 0.6530 (ttpt) REVERT: A 153 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8473 (t) REVERT: A 618 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7780 (tm-30) REVERT: A 627 ARG cc_start: 0.7820 (mtt90) cc_final: 0.7504 (mtt-85) REVERT: A 660 ARG cc_start: 0.6665 (mtm180) cc_final: 0.4920 (ttm110) REVERT: A 702 GLN cc_start: 0.7349 (OUTLIER) cc_final: 0.7018 (tp-100) REVERT: A 754 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8344 (mt) REVERT: A 771 MET cc_start: -0.1340 (mmt) cc_final: -0.1579 (mtt) REVERT: A 776 TYR cc_start: 0.5774 (OUTLIER) cc_final: 0.3709 (m-80) outliers start: 11 outliers final: 5 residues processed: 57 average time/residue: 0.1149 time to fit residues: 8.8746 Evaluate side-chains 55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 220 CYS 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 754 ILE Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 784 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 53 optimal weight: 0.1980 chunk 7 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 16 optimal weight: 0.1980 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4479 r_free = 0.4479 target = 0.166231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.119521 restraints weight = 21954.728| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 3.19 r_work: 0.3476 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10653 Z= 0.231 Angle : 0.656 10.156 15177 Z= 0.350 Chirality : 0.039 0.178 1778 Planarity : 0.005 0.049 1303 Dihedral : 23.380 132.981 3268 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.35 % Favored : 93.52 % Rotamer: Outliers : 1.57 % Allowed : 16.71 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.31), residues: 787 helix: 1.82 (0.30), residues: 298 sheet: -1.01 (0.46), residues: 130 loop : -1.22 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 615 TYR 0.026 0.002 TYR A 244 PHE 0.017 0.002 PHE A 815 TRP 0.017 0.002 TRP A 86 HIS 0.005 0.001 HIS A 920 Details of bonding type rmsd covalent geometry : bond 0.00514 (10652) covalent geometry : angle 0.65651 (15175) SS BOND : bond 0.00209 ( 1) SS BOND : angle 0.47283 ( 2) hydrogen bonds : bond 0.06461 ( 434) hydrogen bonds : angle 4.36153 ( 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 58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 153 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8404 (t) REVERT: A 618 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7918 (tm-30) REVERT: A 627 ARG cc_start: 0.7937 (mtt90) cc_final: 0.7641 (mtt-85) REVERT: A 660 ARG cc_start: 0.6536 (mtm180) cc_final: 0.4628 (ttm110) REVERT: A 702 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.7291 (tp40) REVERT: A 754 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8402 (mp) REVERT: A 790 GLU cc_start: 0.8268 (mm-30) cc_final: 0.8047 (tp30) outliers start: 11 outliers final: 6 residues processed: 55 average time/residue: 0.1431 time to fit residues: 10.3291 Evaluate side-chains 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 220 CYS 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 754 ILE 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: 0.9980 chunk 7 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 77 optimal weight: 0.0170 chunk 25 optimal weight: 4.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4529 r_free = 0.4529 target = 0.170121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.122720 restraints weight = 21963.756| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.54 r_work: 0.3616 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 10653 Z= 0.119 Angle : 0.560 11.546 15177 Z= 0.300 Chirality : 0.034 0.129 1778 Planarity : 0.004 0.042 1303 Dihedral : 23.182 138.356 3268 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 1.00 % Allowed : 17.43 % Favored : 81.57 % 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 aren not related in a simple way. whole: 0.44 (0.31), residues: 787 helix: 2.16 (0.30), residues: 299 sheet: -0.60 (0.46), residues: 135 loop : -0.99 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 111 TYR 0.015 0.001 TYR A 140 PHE 0.009 0.001 PHE A 509 TRP 0.018 0.001 TRP A 962 HIS 0.002 0.001 HIS A 920 Details of bonding type rmsd covalent geometry : bond 0.00257 (10652) covalent geometry : angle 0.55963 (15175) SS BOND : bond 0.00053 ( 1) SS BOND : angle 0.20923 ( 2) hydrogen bonds : bond 0.04632 ( 434) hydrogen bonds : angle 4.16407 ( 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 53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 618 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7732 (tm-30) REVERT: A 660 ARG cc_start: 0.6443 (mtm180) cc_final: 0.4708 (ttm110) REVERT: A 702 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.6919 (tp-100) REVERT: A 754 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8426 (mp) REVERT: A 790 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7772 (tp30) outliers start: 7 outliers final: 4 residues processed: 49 average time/residue: 0.1117 time to fit residues: 7.5041 Evaluate side-chains 51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 754 ILE Chi-restraints excluded: chain A residue 776 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 43 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 32 optimal weight: 0.0980 chunk 47 optimal weight: 1.9990 chunk 12 optimal weight: 30.0000 chunk 17 optimal weight: 6.9990 chunk 54 optimal weight: 0.0970 chunk 57 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4540 r_free = 0.4540 target = 0.171467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.118385 restraints weight = 22094.929| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 3.02 r_work: 0.3604 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10653 Z= 0.115 Angle : 0.541 12.319 15177 Z= 0.287 Chirality : 0.033 0.135 1778 Planarity : 0.004 0.043 1303 Dihedral : 23.125 141.839 3268 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.32 % Favored : 95.55 % Rotamer: Outliers : 1.00 % Allowed : 17.43 % Favored : 81.57 % 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 aren not related in a simple way. whole: 0.50 (0.32), residues: 787 helix: 2.16 (0.30), residues: 305 sheet: -0.72 (0.45), residues: 147 loop : -0.89 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 337 TYR 0.012 0.001 TYR A 244 PHE 0.009 0.001 PHE A 588 TRP 0.017 0.001 TRP A 304 HIS 0.002 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00248 (10652) covalent geometry : angle 0.54072 (15175) SS BOND : bond 0.00052 ( 1) SS BOND : angle 0.25392 ( 2) hydrogen bonds : bond 0.04402 ( 434) hydrogen bonds : angle 3.97099 ( 1115) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2943.63 seconds wall clock time: 50 minutes 47.24 seconds (3047.24 seconds total)