Starting phenix.real_space_refine on Fri Feb 14 12:55:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wb0_32391/02_2025/7wb0_32391.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wb0_32391/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wb0_32391/02_2025/7wb0_32391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wb0_32391/02_2025/7wb0_32391.map" model { file = "/net/cci-nas-00/data/ceres_data/7wb0_32391/02_2025/7wb0_32391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wb0_32391/02_2025/7wb0_32391.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.96, per 1000 atoms: 0.59 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: 2.52 Conformation dependent library (CDL) restraints added in 914.7 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: 3.46 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: 4.87 Time building geometry restraints manager: 2.94 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: 0.850 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.930 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.270 ------------------------------------------------------------------------------- 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 10652 Z= 0.155 Angle : 0.579 10.444 15175 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.021 0.002 TRP A 304 HIS 0.001 0.001 HIS A 920 PHE 0.006 0.001 PHE A 917 TYR 0.016 0.001 TYR A 698 ARG 0.005 0.000 ARG A 889 *********************** 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 : 0.783 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2194 time to fit residues: 20.4525 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 : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 20.0000 chunk 55 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.4558 r_free = 0.4558 target = 0.173370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.122364 restraints weight = 21924.425| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 3.21 r_work: 0.3603 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10652 Z= 0.159 Angle : 0.540 6.769 15175 Z= 0.289 Chirality : 0.034 0.152 1778 Planarity : 0.004 0.046 1303 Dihedral : 23.296 148.477 3268 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 0.57 % Allowed : 6.29 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.31), residues: 787 helix: 2.22 (0.30), residues: 304 sheet: 0.37 (0.48), residues: 123 loop : -0.91 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 304 HIS 0.002 0.001 HIS A 173 PHE 0.008 0.001 PHE A 588 TYR 0.017 0.001 TYR A 244 ARG 0.003 0.000 ARG A 615 *********************** 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: 4 poor density : 52 time to evaluate : 0.731 Fit side-chains REVERT: A 141 LYS cc_start: 0.6793 (ttmt) cc_final: 0.6185 (ttpt) REVERT: A 618 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7810 (tm-30) REVERT: A 627 ARG cc_start: 0.8117 (mtt90) cc_final: 0.7659 (mtt-85) REVERT: A 709 LYS cc_start: 0.7507 (ttmt) cc_final: 0.7075 (tttm) outliers start: 4 outliers final: 1 residues processed: 55 average time/residue: 0.2881 time to fit residues: 21.6893 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 : 0.894 ------------------------------------------------------------------------------- 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 90 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 924 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.168985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.113722 restraints weight = 22134.359| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 3.12 r_work: 0.3525 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10652 Z= 0.290 Angle : 0.624 8.188 15175 Z= 0.333 Chirality : 0.038 0.173 1778 Planarity : 0.005 0.059 1303 Dihedral : 23.343 135.196 3268 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.83 % Favored : 95.04 % Rotamer: Outliers : 1.00 % Allowed : 9.86 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.30), residues: 787 helix: 1.97 (0.30), residues: 298 sheet: -0.20 (0.46), residues: 133 loop : -1.17 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 86 HIS 0.004 0.001 HIS A 920 PHE 0.014 0.002 PHE A 588 TYR 0.027 0.002 TYR A 244 ARG 0.015 0.001 ARG A 615 *********************** 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 60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: A 141 LYS cc_start: 0.6872 (ttmt) cc_final: 0.6460 (ttpp) REVERT: A 247 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7543 (tp) REVERT: A 529 LEU cc_start: 0.8504 (mt) cc_final: 0.8203 (mt) REVERT: A 627 ARG cc_start: 0.8223 (mtt90) cc_final: 0.7718 (mtt-85) REVERT: A 660 ARG cc_start: 0.6407 (mtm180) cc_final: 0.4609 (ttm110) REVERT: A 709 LYS cc_start: 0.7669 (ttmt) cc_final: 0.7292 (tttt) outliers start: 7 outliers final: 4 residues processed: 59 average time/residue: 0.2918 time to fit residues: 23.2717 Evaluate side-chains 51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 698 TYR Chi-restraints excluded: chain A residue 702 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 57 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 85 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 chunk 88 optimal weight: 0.0980 chunk 63 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.171813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.122598 restraints weight = 21959.968| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.93 r_work: 0.3573 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10652 Z= 0.149 Angle : 0.526 7.695 15175 Z= 0.284 Chirality : 0.034 0.133 1778 Planarity : 0.004 0.049 1303 Dihedral : 23.191 138.974 3268 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.43 % Favored : 96.44 % Rotamer: Outliers : 0.86 % Allowed : 11.43 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.31), residues: 787 helix: 2.31 (0.30), residues: 298 sheet: -0.35 (0.45), residues: 138 loop : -1.03 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 304 HIS 0.003 0.001 HIS A 251 PHE 0.008 0.001 PHE A 588 TYR 0.017 0.001 TYR A 244 ARG 0.007 0.000 ARG A 615 *********************** 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 60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.887 Fit side-chains REVERT: A 141 LYS cc_start: 0.6910 (ttmt) cc_final: 0.6482 (ttpp) REVERT: A 153 THR cc_start: 0.8404 (OUTLIER) cc_final: 0.8031 (t) REVERT: A 234 MET cc_start: 0.8486 (mmp) cc_final: 0.8080 (mmp) REVERT: A 618 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7763 (tm-30) REVERT: A 627 ARG cc_start: 0.8060 (mtt90) cc_final: 0.7643 (mtt-85) REVERT: A 660 ARG cc_start: 0.6473 (mtm180) cc_final: 0.4527 (ttm110) REVERT: A 702 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.6772 (tp-100) REVERT: A 709 LYS cc_start: 0.7757 (ttmt) cc_final: 0.7455 (tttm) REVERT: A 723 TYR cc_start: 0.5181 (m-80) cc_final: 0.4284 (m-80) outliers start: 6 outliers final: 2 residues processed: 58 average time/residue: 0.3292 time to fit residues: 25.2719 Evaluate side-chains 49 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 698 TYR Chi-restraints excluded: chain A residue 702 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 21 optimal weight: 0.9990 chunk 10 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 = 0.4516 r_free = 0.4516 target = 0.169495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.119657 restraints weight = 21995.971| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.84 r_work: 0.3538 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10652 Z= 0.233 Angle : 0.573 8.053 15175 Z= 0.308 Chirality : 0.036 0.139 1778 Planarity : 0.004 0.052 1303 Dihedral : 23.240 136.212 3268 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.45 % Favored : 95.43 % Rotamer: Outliers : 1.71 % Allowed : 12.86 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.31), residues: 787 helix: 2.19 (0.30), residues: 298 sheet: -0.38 (0.45), residues: 137 loop : -1.09 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 86 HIS 0.004 0.001 HIS A 251 PHE 0.013 0.001 PHE A 588 TYR 0.022 0.002 TYR A 244 ARG 0.008 0.001 ARG A 337 *********************** 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 : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 LYS cc_start: 0.6880 (ttmt) cc_final: 0.6459 (ttpp) REVERT: A 153 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8186 (t) REVERT: A 618 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7758 (tm-30) REVERT: A 627 ARG cc_start: 0.8029 (mtt90) cc_final: 0.7580 (mtt-85) REVERT: A 660 ARG cc_start: 0.6487 (mtm180) cc_final: 0.4725 (ttm110) REVERT: A 702 GLN cc_start: 0.7183 (OUTLIER) cc_final: 0.6728 (tp-100) outliers start: 12 outliers final: 5 residues processed: 60 average time/residue: 0.3021 time to fit residues: 24.5078 Evaluate side-chains 54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 153 THR 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 813 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 82 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.4522 r_free = 0.4522 target = 0.170093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.120872 restraints weight = 22007.983| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.99 r_work: 0.3530 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10652 Z= 0.195 Angle : 0.555 7.960 15175 Z= 0.299 Chirality : 0.035 0.139 1778 Planarity : 0.004 0.049 1303 Dihedral : 23.214 136.844 3268 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.07 % Favored : 95.81 % Rotamer: Outliers : 1.86 % Allowed : 12.86 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.31), residues: 787 helix: 2.24 (0.30), residues: 298 sheet: -0.39 (0.45), residues: 135 loop : -1.11 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 304 HIS 0.005 0.001 HIS A 251 PHE 0.012 0.001 PHE A 588 TYR 0.018 0.001 TYR A 244 ARG 0.005 0.000 ARG A 615 *********************** 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 62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.869 Fit side-chains REVERT: A 141 LYS cc_start: 0.6892 (ttmt) cc_final: 0.6443 (ttpp) REVERT: A 153 THR cc_start: 0.8547 (OUTLIER) cc_final: 0.8203 (t) REVERT: A 234 MET cc_start: 0.8584 (mmp) cc_final: 0.8136 (mmp) REVERT: A 247 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7555 (tp) REVERT: A 618 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7748 (tm-30) REVERT: A 627 ARG cc_start: 0.7975 (mtt90) cc_final: 0.7639 (mtt-85) REVERT: A 660 ARG cc_start: 0.6583 (mtm180) cc_final: 0.4906 (ttm110) REVERT: A 702 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.6783 (tp-100) REVERT: A 776 TYR cc_start: 0.5569 (OUTLIER) cc_final: 0.3542 (m-80) outliers start: 13 outliers final: 5 residues processed: 59 average time/residue: 0.2842 time to fit residues: 22.9262 Evaluate side-chains 57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 41 optimal weight: 5.9990 chunk 81 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 74 optimal weight: 0.2980 chunk 6 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.171252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.122879 restraints weight = 22145.759| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.81 r_work: 0.3566 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10652 Z= 0.156 Angle : 0.526 7.679 15175 Z= 0.285 Chirality : 0.034 0.137 1778 Planarity : 0.004 0.048 1303 Dihedral : 23.157 138.917 3268 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.19 % Favored : 95.68 % Rotamer: Outliers : 1.43 % Allowed : 14.57 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.31), residues: 787 helix: 2.13 (0.30), residues: 305 sheet: -0.36 (0.45), residues: 137 loop : -0.97 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 304 HIS 0.003 0.001 HIS A 251 PHE 0.009 0.001 PHE A 588 TYR 0.015 0.001 TYR A 244 ARG 0.006 0.000 ARG A 337 *********************** 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 62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 141 LYS cc_start: 0.6911 (ttmt) cc_final: 0.6478 (ttpp) REVERT: A 153 THR cc_start: 0.8597 (OUTLIER) cc_final: 0.8307 (t) REVERT: A 234 MET cc_start: 0.8512 (mmp) cc_final: 0.8097 (mmp) REVERT: A 247 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7498 (tp) REVERT: A 627 ARG cc_start: 0.7825 (mtt90) cc_final: 0.7410 (mtt-85) REVERT: A 660 ARG cc_start: 0.6477 (mtm180) cc_final: 0.4830 (ttm110) REVERT: A 702 GLN cc_start: 0.6932 (OUTLIER) cc_final: 0.6612 (tp-100) REVERT: A 754 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8313 (mp) outliers start: 10 outliers final: 5 residues processed: 59 average time/residue: 0.3123 time to fit residues: 24.6318 Evaluate side-chains 54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE 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 570 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 46 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 20.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 520 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.170877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.118786 restraints weight = 22096.004| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 3.14 r_work: 0.3563 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10652 Z= 0.175 Angle : 0.538 9.001 15175 Z= 0.289 Chirality : 0.034 0.135 1778 Planarity : 0.004 0.047 1303 Dihedral : 23.152 138.515 3268 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.19 % Favored : 95.68 % Rotamer: Outliers : 2.00 % Allowed : 14.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.31), residues: 787 helix: 2.14 (0.30), residues: 305 sheet: -0.41 (0.46), residues: 137 loop : -0.96 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 304 HIS 0.004 0.001 HIS A 251 PHE 0.011 0.001 PHE A 588 TYR 0.017 0.001 TYR A 244 ARG 0.004 0.000 ARG A 615 *********************** 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 62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: A 141 LYS cc_start: 0.6837 (ttmt) cc_final: 0.6389 (ttpp) REVERT: A 153 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8375 (t) REVERT: A 234 MET cc_start: 0.8525 (mmp) cc_final: 0.8103 (mmp) REVERT: A 247 ILE cc_start: 0.7907 (OUTLIER) cc_final: 0.7496 (tp) REVERT: A 618 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7767 (tm-30) REVERT: A 627 ARG cc_start: 0.7834 (mtt90) cc_final: 0.7463 (mtt-85) REVERT: A 660 ARG cc_start: 0.6501 (mtm180) cc_final: 0.4753 (ttm110) REVERT: A 754 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8286 (mp) outliers start: 14 outliers final: 6 residues processed: 57 average time/residue: 0.3038 time to fit residues: 23.4975 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 : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE 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 668 ILE Chi-restraints excluded: chain A residue 698 TYR Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 779 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 = 0.169260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.115114 restraints weight = 21977.072| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.98 r_work: 0.3544 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10652 Z= 0.223 Angle : 0.570 7.993 15175 Z= 0.307 Chirality : 0.036 0.144 1778 Planarity : 0.004 0.047 1303 Dihedral : 23.200 136.653 3268 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.19 % Favored : 95.68 % Rotamer: Outliers : 1.86 % Allowed : 15.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.31), residues: 787 helix: 2.20 (0.30), residues: 299 sheet: -0.65 (0.45), residues: 137 loop : -1.01 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 304 HIS 0.005 0.001 HIS A 251 PHE 0.012 0.001 PHE A 588 TYR 0.020 0.002 TYR A 244 ARG 0.004 0.000 ARG A 615 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: A 141 LYS cc_start: 0.6852 (ttmt) cc_final: 0.6510 (ttpt) REVERT: A 153 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8511 (t) REVERT: A 247 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7527 (tp) REVERT: A 306 ASN cc_start: 0.6786 (t0) cc_final: 0.6510 (t0) REVERT: A 618 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7804 (tm-30) REVERT: A 627 ARG cc_start: 0.7927 (mtt90) cc_final: 0.7554 (mtt-85) REVERT: A 660 ARG cc_start: 0.6390 (mtm180) cc_final: 0.4923 (ttm110) REVERT: A 754 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8332 (mp) outliers start: 13 outliers final: 9 residues processed: 56 average time/residue: 0.3037 time to fit residues: 23.0931 Evaluate side-chains 57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 114 ILE 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 570 MET Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 698 TYR 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 10 optimal weight: 20.0000 chunk 56 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 28 optimal weight: 20.0000 chunk 42 optimal weight: 8.9990 chunk 21 optimal weight: 0.0770 chunk 22 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.171490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.123638 restraints weight = 21852.916| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.86 r_work: 0.3612 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 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 : 0.002 0.026 10652 Z= 0.146 Angle : 0.526 8.828 15175 Z= 0.283 Chirality : 0.033 0.127 1778 Planarity : 0.004 0.046 1303 Dihedral : 23.117 139.636 3268 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.32 % Favored : 95.55 % Rotamer: Outliers : 1.43 % Allowed : 15.57 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.31), residues: 787 helix: 2.42 (0.30), residues: 299 sheet: -0.53 (0.45), residues: 137 loop : -0.87 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 304 HIS 0.003 0.001 HIS A 251 PHE 0.009 0.001 PHE A 588 TYR 0.014 0.001 TYR A 244 ARG 0.004 0.000 ARG A 615 ********************** 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 58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: A 141 LYS cc_start: 0.6887 (ttmt) cc_final: 0.6443 (ttpp) REVERT: A 234 MET cc_start: 0.8497 (mmp) cc_final: 0.8060 (mmp) REVERT: A 247 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7480 (tp) REVERT: A 618 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7773 (tm-30) REVERT: A 627 ARG cc_start: 0.7858 (mtt90) cc_final: 0.7462 (mtt-85) REVERT: A 660 ARG cc_start: 0.6416 (mtm180) cc_final: 0.4819 (ttm110) outliers start: 10 outliers final: 7 residues processed: 55 average time/residue: 0.2980 time to fit residues: 22.1218 Evaluate side-chains 54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 698 TYR 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 50 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 31 optimal weight: 0.0770 chunk 37 optimal weight: 6.9990 chunk 84 optimal weight: 0.4980 chunk 85 optimal weight: 0.0870 chunk 86 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.5320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.173500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.124299 restraints weight = 21994.967| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 3.21 r_work: 0.3610 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10652 Z= 0.130 Angle : 0.510 9.427 15175 Z= 0.274 Chirality : 0.033 0.128 1778 Planarity : 0.004 0.045 1303 Dihedral : 23.040 145.472 3268 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.56 % Favored : 96.32 % Rotamer: Outliers : 1.57 % Allowed : 15.14 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.32), residues: 787 helix: 2.37 (0.30), residues: 306 sheet: -0.46 (0.44), residues: 149 loop : -0.77 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 304 HIS 0.003 0.001 HIS A 251 PHE 0.006 0.001 PHE A 509 TYR 0.010 0.001 TYR A 944 ARG 0.004 0.000 ARG A 337 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6295.08 seconds wall clock time: 111 minutes 42.00 seconds (6702.00 seconds total)