Starting phenix.real_space_refine on Fri Jul 3 02:41:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d2p_27145/07_2026/8d2p_27145.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2p_27145/07_2026/8d2p_27145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d2p_27145/07_2026/8d2p_27145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2p_27145/07_2026/8d2p_27145.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d2p_27145/07_2026/8d2p_27145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2p_27145/07_2026/8d2p_27145.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8d2p_27145/07_2026/8d2p_27145.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d2p_27145/07_2026/8d2p_27145.cif" } resolution = 2.78 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 128 5.49 5 Mg 10 5.21 5 S 20 5.16 5 C 6655 2.51 5 N 2109 2.21 5 O 2514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11436 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8720 Classifications: {'peptide': 1105} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 59, 'TRANS': 1041} Chain breaks: 3 Chain: "B" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 2189 Unusual residues: {'GTP': 1} Classifications: {'RNA': 101, 'undetermined': 1} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 46, 'rna3p_pyr': 42} Link IDs: {'rna2p': 13, 'rna3p': 87, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" G B 2 " Chain breaks: 1 Chain: "T" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 481 Classifications: {'DNA': 24} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' MG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "T" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 2.14, per 1000 atoms: 0.19 Number of scatterers: 11436 At special positions: 0 Unit cell: (94.05, 106.425, 130.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 20 16.00 P 128 15.00 Mg 10 11.99 O 2514 8.00 N 2109 7.00 C 6655 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 429.8 milliseconds 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 8 sheets defined 49.9% alpha, 8.8% beta 41 base pairs and 80 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 59 through 92 Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 120 through 138 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 180 through 192 Processing helix chain 'A' and resid 221 through 237 removed outlier: 3.569A pdb=" N VAL A 225 " --> pdb=" O ARG A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 251 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 279 through 293 Processing helix chain 'A' and resid 306 through 319 Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 364 through 377 Processing helix chain 'A' and resid 381 through 391 Processing helix chain 'A' and resid 392 through 405 Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 421 through 430 Processing helix chain 'A' and resid 441 through 456 Processing helix chain 'A' and resid 458 through 468 Processing helix chain 'A' and resid 486 through 508 Processing helix chain 'A' and resid 524 through 552 Processing helix chain 'A' and resid 558 through 571 Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 611 through 618 Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 633 through 643 Processing helix chain 'A' and resid 653 through 669 Processing helix chain 'A' and resid 681 through 703 Processing helix chain 'A' and resid 711 through 721 removed outlier: 3.976A pdb=" N THR A 715 " --> pdb=" O ARG A 711 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA A 716 " --> pdb=" O GLY A 712 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU A 717 " --> pdb=" O GLY A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 730 Processing helix chain 'A' and resid 742 through 747 removed outlier: 4.009A pdb=" N LEU A 745 " --> pdb=" O THR A 742 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP A 746 " --> pdb=" O LYS A 743 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ARG A 747 " --> pdb=" O ARG A 744 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 742 through 747' Processing helix chain 'A' and resid 748 through 758 Processing helix chain 'A' and resid 761 through 777 Processing helix chain 'A' and resid 797 through 807 Processing helix chain 'A' and resid 809 through 820 removed outlier: 3.690A pdb=" N ARG A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 860 Processing helix chain 'A' and resid 864 through 876 Processing helix chain 'A' and resid 957 through 963 Processing helix chain 'A' and resid 981 through 986 Processing helix chain 'A' and resid 988 through 997 Processing helix chain 'A' and resid 1025 through 1030 Processing helix chain 'A' and resid 1058 through 1068 Processing helix chain 'A' and resid 1076 through 1086 Processing helix chain 'A' and resid 1093 through 1098 Processing sheet with id=AA1, first strand: chain 'A' and resid 706 through 710 removed outlier: 6.370A pdb=" N ILE A 513 " --> pdb=" O ALA A 708 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N PHE A 710 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A 515 " --> pdb=" O PHE A 710 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TRP A 13 " --> pdb=" O SER A 512 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N VAL A 514 " --> pdb=" O TRP A 13 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU A 15 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N GLU A 516 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL A 17 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE A 24 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A 43 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU A 26 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA A 41 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA A 28 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ILE A 39 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER A 30 " --> pdb=" O LYS A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 301 through 304 Processing sheet with id=AA3, first strand: chain 'A' and resid 588 through 591 Processing sheet with id=AA4, first strand: chain 'A' and resid 846 through 849 Processing sheet with id=AA5, first strand: chain 'A' and resid 854 through 855 Processing sheet with id=AA6, first strand: chain 'A' and resid 921 through 924 Processing sheet with id=AA7, first strand: chain 'A' and resid 948 through 956 removed outlier: 3.738A pdb=" N GLY A1004 " --> pdb=" O VAL A 939 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG A 941 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N GLN A1002 " --> pdb=" O ARG A 941 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1090 through 1091 removed outlier: 6.748A pdb=" N ASN A1050 " --> pdb=" O THR A1041 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU A1011 " --> pdb=" O ILE A1106 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 106 hydrogen bonds 200 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 80 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 1.17 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: 2585 1.33 - 1.45: 3122 1.45 - 1.57: 5902 1.57 - 1.69: 252 1.69 - 1.81: 28 Bond restraints: 11889 Sorted by residual: bond pdb=" C1' DC T 21 " pdb=" N1 DC T 21 " ideal model delta sigma weight residual 1.468 1.558 -0.090 1.40e-02 5.10e+03 4.12e+01 bond pdb=" C1' DT T 37 " pdb=" N1 DT T 37 " ideal model delta sigma weight residual 1.468 1.529 -0.061 1.40e-02 5.10e+03 1.87e+01 bond pdb=" C3' DC T 36 " pdb=" O3' DC T 36 " ideal model delta sigma weight residual 1.435 1.486 -0.051 1.30e-02 5.92e+03 1.55e+01 bond pdb=" N1 DC T 21 " pdb=" C2 DC T 21 " ideal model delta sigma weight residual 1.397 1.428 -0.031 1.00e-02 1.00e+04 9.89e+00 bond pdb=" C1' DT T 20 " pdb=" N1 DT T 20 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.24e+00 ... (remaining 11884 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 16217 2.11 - 4.23: 438 4.23 - 6.34: 52 6.34 - 8.46: 15 8.46 - 10.57: 2 Bond angle restraints: 16724 Sorted by residual: angle pdb=" O4' DC T 21 " pdb=" C1' DC T 21 " pdb=" N1 DC T 21 " ideal model delta sigma weight residual 108.00 113.79 -5.79 7.00e-01 2.04e+00 6.84e+01 angle pdb=" O4' DG T 17 " pdb=" C1' DG T 17 " pdb=" N9 DG T 17 " ideal model delta sigma weight residual 108.00 112.30 -4.30 7.00e-01 2.04e+00 3.78e+01 angle pdb=" C4' DG T 17 " pdb=" O4' DG T 17 " pdb=" C1' DG T 17 " ideal model delta sigma weight residual 110.10 104.75 5.35 1.00e+00 1.00e+00 2.87e+01 angle pdb=" CG ARG A 323 " pdb=" CD ARG A 323 " pdb=" NE ARG A 323 " ideal model delta sigma weight residual 112.00 122.57 -10.57 2.20e+00 2.07e-01 2.31e+01 angle pdb=" C1' DC T 21 " pdb=" N1 DC T 21 " pdb=" C2 DC T 21 " ideal model delta sigma weight residual 118.80 124.08 -5.28 1.10e+00 8.26e-01 2.31e+01 ... (remaining 16719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.86: 6737 29.86 - 59.71: 330 59.71 - 89.57: 120 89.57 - 119.42: 3 119.42 - 149.28: 3 Dihedral angle restraints: 7193 sinusoidal: 3997 harmonic: 3196 Sorted by residual: dihedral pdb=" C5' GTP B 1 " pdb=" O5' GTP B 1 " pdb=" PA GTP B 1 " pdb=" O3A GTP B 1 " ideal model delta sinusoidal sigma weight residual 69.27 162.88 -93.61 1 2.00e+01 2.50e-03 2.55e+01 dihedral pdb=" C8 GTP B 1 " pdb=" C1' GTP B 1 " pdb=" N9 GTP B 1 " pdb=" O4' GTP B 1 " ideal model delta sinusoidal sigma weight residual 104.59 13.60 90.99 1 2.00e+01 2.50e-03 2.44e+01 dihedral pdb=" CA ILE A 592 " pdb=" C ILE A 592 " pdb=" N VAL A 593 " pdb=" CA VAL A 593 " ideal model delta harmonic sigma weight residual 180.00 157.55 22.45 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 7190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1572 0.058 - 0.116: 304 0.116 - 0.175: 43 0.175 - 0.233: 8 0.233 - 0.291: 3 Chirality restraints: 1930 Sorted by residual: chirality pdb=" CG LEU A 84 " pdb=" CB LEU A 84 " pdb=" CD1 LEU A 84 " pdb=" CD2 LEU A 84 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CG LEU A1075 " pdb=" CB LEU A1075 " pdb=" CD1 LEU A1075 " pdb=" CD2 LEU A1075 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C1' G B 30 " pdb=" O4' G B 30 " pdb=" C2' G B 30 " pdb=" N9 G B 30 " both_signs ideal model delta sigma weight residual False 2.46 2.21 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 1927 not shown) Planarity restraints: 1714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 363 " 0.024 2.00e-02 2.50e+03 3.23e-02 1.82e+01 pdb=" CG PHE A 363 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 PHE A 363 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 PHE A 363 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 363 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE A 363 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A 363 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 800 " 0.009 2.00e-02 2.50e+03 1.96e-02 7.68e+00 pdb=" CG TYR A 800 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A 800 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 800 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR A 800 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 800 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 800 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 800 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 187 " -0.001 2.00e-02 2.50e+03 1.95e-02 7.60e+00 pdb=" CG TYR A 187 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 187 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR A 187 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR A 187 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 187 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 187 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 187 " -0.014 2.00e-02 2.50e+03 ... (remaining 1711 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 134 2.59 - 3.17: 8583 3.17 - 3.75: 20848 3.75 - 4.32: 27910 4.32 - 4.90: 42434 Nonbonded interactions: 99909 Sorted by model distance: nonbonded pdb="MG MG A1201 " pdb=" O HOH A1304 " model vdw 2.018 2.170 nonbonded pdb=" OD1 ASP A 590 " pdb="MG MG A1201 " model vdw 2.021 2.170 nonbonded pdb=" OP2 DC T 14 " pdb="MG MG A1201 " model vdw 2.036 2.170 nonbonded pdb=" OD1 ASN A 614 " pdb="MG MG A1201 " model vdw 2.045 2.170 nonbonded pdb="MG MG B 202 " pdb=" O HOH B 312 " model vdw 2.085 2.170 ... (remaining 99904 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=0.00 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: 2.510 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: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.500 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: 0.000 Load rotamer database and sin/cos tables:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 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 : 0.005 0.090 11891 Z= 0.283 Angle : 0.823 10.570 16724 Z= 0.481 Chirality : 0.048 0.291 1930 Planarity : 0.008 0.108 1714 Dihedral : 18.207 149.279 5119 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.22), residues: 1097 helix: -0.68 (0.19), residues: 528 sheet: -0.70 (0.48), residues: 89 loop : -0.81 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 544 TYR 0.047 0.004 TYR A 800 PHE 0.069 0.003 PHE A 363 TRP 0.022 0.002 TRP A 161 HIS 0.005 0.002 HIS A1037 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.28 (11889) covalent geometry : angle 0.82254 / 0.48 (16724) hydrogen bonds : bond 0.06535 / 4.62 ( 522) hydrogen bonds : angle 5.30919 / 3.88 ( 1409) Misc. bond : bond 0.00168 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.349 Fit side-chains REVERT: A 155 PRO cc_start: 0.7570 (Cg_endo) cc_final: 0.7300 (Cg_exo) REVERT: A 572 ASP cc_start: 0.7804 (t0) cc_final: 0.7578 (t0) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.8342 time to fit residues: 100.6959 Evaluate side-chains 84 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.0970 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.0030 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.172136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.149325 restraints weight = 11942.310| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.07 r_work: 0.3208 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11891 Z= 0.126 Angle : 0.541 6.295 16724 Z= 0.290 Chirality : 0.038 0.263 1930 Planarity : 0.005 0.069 1714 Dihedral : 18.705 152.131 3030 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.08 % Allowed : 6.23 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.24), residues: 1097 helix: 0.73 (0.22), residues: 529 sheet: -0.77 (0.49), residues: 89 loop : -0.51 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 303 TYR 0.015 0.002 TYR A 800 PHE 0.016 0.001 PHE A 282 TRP 0.013 0.001 TRP A 387 HIS 0.003 0.001 HIS A1100 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.13 (11889) covalent geometry : angle 0.54148 / 0.29 (16724) hydrogen bonds : bond 0.05025 / 3.53 ( 522) hydrogen bonds : angle 4.39331 / 3.27 ( 1409) Misc. bond : bond 0.00175 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 155 PRO cc_start: 0.7495 (Cg_endo) cc_final: 0.7225 (Cg_exo) REVERT: A 470 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7327 (p0) REVERT: A 572 ASP cc_start: 0.8040 (t0) cc_final: 0.7595 (t0) REVERT: A 597 ASP cc_start: 0.8155 (m-30) cc_final: 0.7912 (m-30) REVERT: A 802 GLN cc_start: 0.7019 (OUTLIER) cc_final: 0.6782 (pm20) outliers start: 19 outliers final: 5 residues processed: 108 average time/residue: 0.7839 time to fit residues: 90.0411 Evaluate side-chains 100 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 802 GLN Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 1064 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 55 optimal weight: 7.9990 chunk 90 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.167882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.132881 restraints weight = 11970.846| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.14 r_work: 0.3217 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11891 Z= 0.166 Angle : 0.562 6.072 16724 Z= 0.300 Chirality : 0.040 0.246 1930 Planarity : 0.005 0.071 1714 Dihedral : 18.608 150.401 3030 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.86 % Allowed : 7.76 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.24), residues: 1097 helix: 1.13 (0.22), residues: 535 sheet: -0.88 (0.48), residues: 89 loop : -0.42 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 720 TYR 0.012 0.002 TYR A 868 PHE 0.021 0.002 PHE A 282 TRP 0.020 0.002 TRP A 387 HIS 0.005 0.001 HIS A1100 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 (11889) covalent geometry : angle 0.56215 / 0.30 (16724) hydrogen bonds : bond 0.05143 / 3.60 ( 522) hydrogen bonds : angle 4.20257 / 3.12 ( 1409) Misc. bond : bond 0.00190 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.379 Fit side-chains REVERT: A 155 PRO cc_start: 0.7504 (Cg_endo) cc_final: 0.7247 (Cg_exo) REVERT: A 470 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.7348 (p0) REVERT: A 572 ASP cc_start: 0.8167 (t0) cc_final: 0.7698 (t0) REVERT: A 597 ASP cc_start: 0.8135 (m-30) cc_final: 0.7906 (m-30) outliers start: 17 outliers final: 6 residues processed: 107 average time/residue: 0.8176 time to fit residues: 92.8553 Evaluate side-chains 98 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 949 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 120 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 99 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.164918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.142465 restraints weight = 11898.977| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.08 r_work: 0.3110 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11891 Z= 0.250 Angle : 0.646 5.692 16724 Z= 0.341 Chirality : 0.044 0.301 1930 Planarity : 0.006 0.072 1714 Dihedral : 18.703 150.221 3030 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.62 % Allowed : 9.40 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.24), residues: 1097 helix: 0.99 (0.22), residues: 536 sheet: -0.88 (0.48), residues: 91 loop : -0.45 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 772 TYR 0.014 0.003 TYR A 187 PHE 0.026 0.003 PHE A 282 TRP 0.021 0.002 TRP A 387 HIS 0.009 0.002 HIS A1100 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.25 (11889) covalent geometry : angle 0.64595 / 0.34 (16724) hydrogen bonds : bond 0.05632 / 3.92 ( 522) hydrogen bonds : angle 4.42381 / 3.27 ( 1409) Misc. bond : bond 0.00206 / 0.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.366 Fit side-chains REVERT: A 155 PRO cc_start: 0.7499 (Cg_endo) cc_final: 0.7227 (Cg_exo) REVERT: A 261 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7224 (pm20) REVERT: A 398 ASP cc_start: 0.6858 (OUTLIER) cc_final: 0.6205 (m-30) REVERT: A 572 ASP cc_start: 0.8170 (t0) cc_final: 0.7677 (t0) REVERT: A 654 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6873 (mmt90) REVERT: A 801 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.6721 (mtp180) REVERT: A 1052 LYS cc_start: 0.8196 (pttt) cc_final: 0.7666 (pttp) outliers start: 24 outliers final: 10 residues processed: 108 average time/residue: 0.7905 time to fit residues: 90.5444 Evaluate side-chains 103 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 801 ARG Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1064 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 80 optimal weight: 0.2980 chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 320 GLN A 472 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.166207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.135080 restraints weight = 11953.486| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.52 r_work: 0.3128 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11891 Z= 0.182 Angle : 0.578 6.284 16724 Z= 0.308 Chirality : 0.041 0.255 1930 Planarity : 0.005 0.072 1714 Dihedral : 18.675 150.075 3030 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.40 % Allowed : 10.05 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.24), residues: 1097 helix: 1.16 (0.22), residues: 536 sheet: -0.96 (0.48), residues: 91 loop : -0.38 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1088 TYR 0.013 0.002 TYR A 31 PHE 0.020 0.002 PHE A 282 TRP 0.022 0.002 TRP A 387 HIS 0.006 0.001 HIS A1100 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (11889) covalent geometry : angle 0.57830 / 0.31 (16724) hydrogen bonds : bond 0.05199 / 3.64 ( 522) hydrogen bonds : angle 4.26877 / 3.16 ( 1409) Misc. bond : bond 0.00190 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.222 Fit side-chains REVERT: A 155 PRO cc_start: 0.7442 (Cg_endo) cc_final: 0.7156 (Cg_exo) REVERT: A 166 GLU cc_start: 0.7674 (tt0) cc_final: 0.7473 (tt0) REVERT: A 261 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7142 (pm20) REVERT: A 398 ASP cc_start: 0.6803 (OUTLIER) cc_final: 0.6127 (m-30) REVERT: A 572 ASP cc_start: 0.8139 (t0) cc_final: 0.7636 (t0) REVERT: A 597 ASP cc_start: 0.8093 (m-30) cc_final: 0.7879 (m-30) REVERT: A 654 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6652 (mmt90) REVERT: A 719 ARG cc_start: 0.6965 (ttp-110) cc_final: 0.6711 (mtm-85) REVERT: A 801 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6736 (mtp180) REVERT: A 880 ARG cc_start: 0.6544 (ptt180) cc_final: 0.5811 (ptt90) REVERT: A 1052 LYS cc_start: 0.8143 (pttt) cc_final: 0.7524 (pttp) outliers start: 22 outliers final: 8 residues processed: 109 average time/residue: 0.7664 time to fit residues: 88.6629 Evaluate side-chains 102 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 801 ARG Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1099 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 0.7980 chunk 98 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 39 optimal weight: 20.0000 chunk 79 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.166339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.143965 restraints weight = 11973.833| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.02 r_work: 0.3159 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11891 Z= 0.178 Angle : 0.572 6.681 16724 Z= 0.305 Chirality : 0.040 0.249 1930 Planarity : 0.005 0.072 1714 Dihedral : 18.639 150.217 3030 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.86 % Allowed : 10.93 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.25), residues: 1097 helix: 1.28 (0.22), residues: 535 sheet: -0.95 (0.48), residues: 91 loop : -0.36 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1088 TYR 0.013 0.002 TYR A 800 PHE 0.019 0.002 PHE A 282 TRP 0.023 0.002 TRP A 387 HIS 0.006 0.001 HIS A1100 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 (11889) covalent geometry : angle 0.57238 / 0.30 (16724) hydrogen bonds : bond 0.05117 / 3.58 ( 522) hydrogen bonds : angle 4.19750 / 3.11 ( 1409) Misc. bond : bond 0.00193 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.354 Fit side-chains REVERT: A 135 MET cc_start: 0.8457 (mtt) cc_final: 0.8234 (mtt) REVERT: A 166 GLU cc_start: 0.7617 (tt0) cc_final: 0.7415 (tt0) REVERT: A 174 VAL cc_start: 0.7927 (p) cc_final: 0.7560 (m) REVERT: A 261 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7084 (pm20) REVERT: A 398 ASP cc_start: 0.6750 (OUTLIER) cc_final: 0.6060 (m-30) REVERT: A 572 ASP cc_start: 0.8080 (t0) cc_final: 0.7545 (t0) REVERT: A 597 ASP cc_start: 0.8061 (m-30) cc_final: 0.7856 (m-30) REVERT: A 719 ARG cc_start: 0.6933 (ttp-110) cc_final: 0.6705 (mtm-85) REVERT: A 801 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6732 (mtp180) REVERT: A 880 ARG cc_start: 0.6569 (ptt180) cc_final: 0.5824 (ptt90) REVERT: A 1052 LYS cc_start: 0.8096 (pttt) cc_final: 0.7468 (pttp) REVERT: A 1118 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7408 (mtm-85) outliers start: 17 outliers final: 9 residues processed: 101 average time/residue: 0.8476 time to fit residues: 90.6543 Evaluate side-chains 107 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 801 ARG Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1099 CYS Chi-restraints excluded: chain A residue 1118 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 84 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 750 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.165663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.143458 restraints weight = 11903.215| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.02 r_work: 0.3145 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11891 Z= 0.198 Angle : 0.592 6.756 16724 Z= 0.315 Chirality : 0.041 0.263 1930 Planarity : 0.005 0.072 1714 Dihedral : 18.629 150.229 3030 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.86 % Allowed : 11.15 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.25), residues: 1097 helix: 1.25 (0.22), residues: 535 sheet: -0.99 (0.47), residues: 91 loop : -0.37 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1088 TYR 0.013 0.002 TYR A 800 PHE 0.020 0.002 PHE A 282 TRP 0.026 0.002 TRP A 387 HIS 0.006 0.001 HIS A1100 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.20 (11889) covalent geometry : angle 0.59199 / 0.31 (16724) hydrogen bonds : bond 0.05222 / 3.65 ( 522) hydrogen bonds : angle 4.22280 / 3.12 ( 1409) Misc. bond : bond 0.00189 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.383 Fit side-chains REVERT: A 166 GLU cc_start: 0.7636 (tt0) cc_final: 0.7429 (tt0) REVERT: A 174 VAL cc_start: 0.7922 (p) cc_final: 0.7547 (m) REVERT: A 261 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7029 (pm20) REVERT: A 398 ASP cc_start: 0.6713 (OUTLIER) cc_final: 0.6058 (m-30) REVERT: A 572 ASP cc_start: 0.8090 (t0) cc_final: 0.7562 (t0) REVERT: A 597 ASP cc_start: 0.8069 (m-30) cc_final: 0.7857 (m-30) REVERT: A 801 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6736 (mtp180) REVERT: A 880 ARG cc_start: 0.6567 (ptt180) cc_final: 0.5818 (ptt90) REVERT: A 1052 LYS cc_start: 0.8095 (pttt) cc_final: 0.7470 (pttp) REVERT: A 1118 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7428 (mtm-85) outliers start: 17 outliers final: 11 residues processed: 105 average time/residue: 0.8514 time to fit residues: 94.8461 Evaluate side-chains 109 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 801 ARG Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1099 CYS Chi-restraints excluded: chain A residue 1118 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 34 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.163969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.132989 restraints weight = 11895.261| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.60 r_work: 0.3091 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 11891 Z= 0.299 Angle : 0.692 7.076 16724 Z= 0.364 Chirality : 0.046 0.328 1930 Planarity : 0.007 0.072 1714 Dihedral : 18.713 150.416 3030 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.30 % Allowed : 11.37 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.24), residues: 1097 helix: 0.84 (0.22), residues: 542 sheet: -1.09 (0.48), residues: 91 loop : -0.45 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 137 TYR 0.017 0.003 TYR A 800 PHE 0.024 0.003 PHE A 282 TRP 0.028 0.002 TRP A 387 HIS 0.008 0.002 HIS A1100 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.30 (11889) covalent geometry : angle 0.69236 / 0.36 (16724) hydrogen bonds : bond 0.05905 / 4.12 ( 522) hydrogen bonds : angle 4.53011 / 3.33 ( 1409) Misc. bond : bond 0.00199 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.355 Fit side-chains REVERT: A 155 PRO cc_start: 0.7503 (Cg_endo) cc_final: 0.7225 (Cg_exo) REVERT: A 261 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7100 (pm20) REVERT: A 398 ASP cc_start: 0.6816 (OUTLIER) cc_final: 0.6128 (m-30) REVERT: A 572 ASP cc_start: 0.8200 (t0) cc_final: 0.7676 (t0) REVERT: A 753 ASP cc_start: 0.7487 (m-30) cc_final: 0.6836 (m-30) REVERT: A 801 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.6711 (mtp180) REVERT: A 880 ARG cc_start: 0.6574 (ptt180) cc_final: 0.5823 (ptt90) REVERT: A 1052 LYS cc_start: 0.8140 (pttt) cc_final: 0.7628 (pttp) REVERT: A 1118 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7453 (mtm-85) outliers start: 21 outliers final: 11 residues processed: 105 average time/residue: 0.8290 time to fit residues: 92.4686 Evaluate side-chains 107 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 801 ARG Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1001 LYS Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1099 CYS Chi-restraints excluded: chain A residue 1118 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 81 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.166434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.143849 restraints weight = 11876.653| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.02 r_work: 0.3128 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11891 Z= 0.163 Angle : 0.574 7.019 16724 Z= 0.306 Chirality : 0.040 0.254 1930 Planarity : 0.005 0.071 1714 Dihedral : 18.641 150.339 3030 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.86 % Allowed : 12.46 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.25), residues: 1097 helix: 1.12 (0.22), residues: 544 sheet: -1.10 (0.48), residues: 91 loop : -0.31 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1088 TYR 0.013 0.002 TYR A 651 PHE 0.018 0.002 PHE A 282 TRP 0.028 0.001 TRP A 387 HIS 0.003 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (11889) covalent geometry : angle 0.57354 / 0.31 (16724) hydrogen bonds : bond 0.05122 / 3.60 ( 522) hydrogen bonds : angle 4.23989 / 3.13 ( 1409) Misc. bond : bond 0.00190 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.272 Fit side-chains REVERT: A 155 PRO cc_start: 0.7306 (Cg_endo) cc_final: 0.7024 (Cg_exo) REVERT: A 166 GLU cc_start: 0.7716 (tt0) cc_final: 0.7506 (tt0) REVERT: A 174 VAL cc_start: 0.7949 (p) cc_final: 0.7584 (m) REVERT: A 261 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7077 (pm20) REVERT: A 398 ASP cc_start: 0.6774 (OUTLIER) cc_final: 0.6082 (m-30) REVERT: A 572 ASP cc_start: 0.8178 (t0) cc_final: 0.7674 (t0) REVERT: A 801 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6731 (mtp180) REVERT: A 880 ARG cc_start: 0.6563 (ptt180) cc_final: 0.5820 (ptt90) REVERT: A 1052 LYS cc_start: 0.8122 (pttt) cc_final: 0.7518 (pttp) REVERT: A 1118 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7439 (mtm-85) outliers start: 17 outliers final: 10 residues processed: 99 average time/residue: 0.8650 time to fit residues: 90.3505 Evaluate side-chains 105 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 801 ARG Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1099 CYS Chi-restraints excluded: chain A residue 1118 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 3 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 49 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1100 HIS A1120 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.169367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.146657 restraints weight = 11970.659| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.05 r_work: 0.3184 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11891 Z= 0.120 Angle : 0.524 6.700 16724 Z= 0.281 Chirality : 0.038 0.260 1930 Planarity : 0.004 0.071 1714 Dihedral : 18.526 150.667 3030 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.77 % Allowed : 13.44 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.25), residues: 1097 helix: 1.46 (0.22), residues: 541 sheet: -1.13 (0.48), residues: 89 loop : -0.22 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1088 TYR 0.013 0.002 TYR A 651 PHE 0.012 0.001 PHE A 282 TRP 0.029 0.001 TRP A 387 HIS 0.005 0.001 HIS A1100 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.12 (11889) covalent geometry : angle 0.52425 / 0.28 (16724) hydrogen bonds : bond 0.04704 / 3.31 ( 522) hydrogen bonds : angle 4.00397 / 2.97 ( 1409) Misc. bond : bond 0.00190 / 0.11 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.7677 (tt0) cc_final: 0.7465 (tt0) REVERT: A 174 VAL cc_start: 0.8004 (p) cc_final: 0.7650 (m) REVERT: A 527 ARG cc_start: 0.6464 (tpp80) cc_final: 0.5852 (ttt90) REVERT: A 572 ASP cc_start: 0.8152 (t0) cc_final: 0.7641 (t0) REVERT: A 719 ARG cc_start: 0.7077 (mtm-85) cc_final: 0.6593 (mtm-85) REVERT: A 880 ARG cc_start: 0.6583 (ptt180) cc_final: 0.5826 (ptt90) REVERT: A 1052 LYS cc_start: 0.8002 (pttt) cc_final: 0.7482 (pttp) outliers start: 7 outliers final: 3 residues processed: 103 average time/residue: 0.8192 time to fit residues: 89.6884 Evaluate side-chains 95 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 949 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 74 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 50 optimal weight: 0.0060 chunk 102 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 98 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 overall best weight: 3.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.165591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.130895 restraints weight = 11937.273| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.12 r_work: 0.3190 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11891 Z= 0.226 Angle : 0.607 6.709 16724 Z= 0.321 Chirality : 0.042 0.264 1930 Planarity : 0.005 0.072 1714 Dihedral : 18.550 150.483 3030 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.09 % Allowed : 13.66 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.25), residues: 1097 helix: 1.21 (0.22), residues: 542 sheet: -1.01 (0.48), residues: 91 loop : -0.26 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 80 TYR 0.015 0.002 TYR A 800 PHE 0.021 0.002 PHE A 282 TRP 0.030 0.002 TRP A 387 HIS 0.004 0.001 HIS A 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.23 (11889) covalent geometry : angle 0.60732 / 0.32 (16724) hydrogen bonds : bond 0.05307 / 3.71 ( 522) hydrogen bonds : angle 4.22261 / 3.12 ( 1409) Misc. bond : bond 0.00198 / 0.11 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3429.51 seconds wall clock time: 59 minutes 24.93 seconds (3564.93 seconds total)